Make sure you installed ‘./DTU’ and ‘./PathCluster’.
if (!require("pacman")) install.packages("pacman")
pacman::p_load(ggpubr, patchwork, ggplotify, VennDiagram, cowplot, matrixStats,
ggrepel, DTU, STRINGdb, knitr, Unicode, readr, DTU, tidyr, dplyr, ggplot2,
viridis, ggridges, aggregation, PathCluster, gridExtra, kableExtra, reshape2,
DRIMSeq, DEXSeq, wiggleplotr)
colorFriendly <- c("pink" = "#CC79A7", "green" = "#009E73", "yellow" = "#F0E442", "orange" = "#E69F00", "blue" = "#0072B2")
reloadDTU <- function(){
detach(name="package:DTU",unload=T);
library(DTU)
} We need the metadata file with all sample information, An output directory for all plots and tables, the qPCR results, the DGE results, and all the rds objects that were produced by “./runDTU.sh”.
# Set output directories
plotOutDir <- "./results/"
tableOutDir <- "./results/"
# meta data file and qPCR result file
metaDataFile <- "./metaData/phenoData.csv"
znfLabFile <- "./results/external/qPCR/ZNF_lab_values.csv"
# Load differential gene expression results from:
# RNASeq paper:
# https://actaneurocomms.biomedcentral.com/articles/10.1186/s40478-020-00932-7
# result object after cell type correction
dge_obj <- readRDS("./results/external/dge_results/DESeqOut_CT.Rds")
names(dge_obj) <-c("discovery","replication")
# check covariate name of condition
DESeq2::resultsNames(dge_obj$discovery)## [1] "Intercept" "sex_M_vs_F" "age_years"
## [4] "rin" "PMI_hours" "Batch_2_vs_1"
## [7] "Batch_3_vs_1" "Batch_4_vs_1" "Profile_PD_vs_Cont"
## [10] "Oligo_Genes" "Microglia_Genes"
# extract result dataframe
dge_results <-list("discovery"=as.data.frame(DESeq2::results(dge_obj$discovery,independentFiltering=T,name="Profile_PD_vs_Cont")) %>%
dplyr::mutate(gene_id = rownames(.)), "replication" = as.data.frame(DESeq2::results(dge_obj$replication,independentFiltering=T,name="Profile_PD_vs_Cont")) %>%
dplyr::mutate(gene_id=rownames(.)))
# after unpacking result objects in ./results/rds/
# Read result object:
# set timestamp to what was defined as paramete in "./runDTU.sh"
# (see filename in ./results/rds/)
timestamp <- "04-05-20"
obj <- readRDS(paste0("./results/rds/obj",timestamp,".rds"))
# read main df of analysis without cell correction
# (Didnt supply the whole object, to prevent making the git repo too big)
# (i.e. cosen covariates where (rin,sex,age_years) without Microglia_Genes, Oligi_Genes.
main_df_no_cc <- readRDS("./results/rds/noCC_main_df.rds")Generating one main dataframe for use of downstream analysis. * Using data from the stageR result list, which has all transcripts and genes that are significant after stageR OFWER correction, i.e. 2 stage testing first the genes and then the transcripts. StageR was applied with alpha==0.05.
* Using the result data frame of both DRIMSeq and DEXSeq which holds the p-values and adjusted p-values, as reported by the respective tool as well as the effect size (i.e. the coefficient of the condition variable). * Using the main data object of both tools, which holds the original counts and or proportions.
# Add sample info and DGE results to the main result object
info <- DTU::create_sample_info(pheno = metaDataFile, cohort_names = c("discovery","replication"), conditions=c("Control","Case")) ## Case Case Control Case Control Case Control Case Control
## 1 1 0 1 0 1 0 1 0
## Case Control Case Control Case Control Case Control Case
## 1 0 1 0 1 0 1 0 1
## Control Case Control Case Case Case Case Case Case
## 0 1 0 1 1 1 1 1 1
## Control
## 0
## Levels: 0 1
## Control Case Control Case Control Case Control Case Control
## 0 1 0 1 0 1 0 1 0
## Case Control Case Control Case Control Case Control Case
## 1 0 1 0 1 0 1 0 1
## Control Control Case
## 0 0 1
## Levels: 0 1
obj$dge <- dge_obj
obj$dge_results <- dge_results
obj$info <- info
# discovery cohort: define df with significant (after correction) (DTU events)
final_disc_dex <- df_disc$dex %>% dplyr::filter(!(is.na(tx_pvalueStageR))) %>%
dplyr::select(tx_id, gene_name, gene_id, l2fc, tx_pvalueStageR, nom_pval, tx_biotype) %>%
dplyr::arrange(abs(l2fc))
final_disc_drim <- df_disc$drim %>% dplyr::filter(!(is.na(tx_pvalueStageR))) %>%
dplyr::select(tx_id, gene_id, gene_name, l2fc, tx_pvalueStageR, nom_pval, tx_biotype) %>%
dplyr::arrange(abs(l2fc))
final_disc_dexdrim <- dplyr::bind_rows("DRIMSeq"= final_disc_drim, "DEXSeq"=final_disc_dex,.id="Tool")
# replication cohort: define df with significant (after correction) (DTU events)
final_repl_dex <- df_repl$dex %>% dplyr::filter(!(is.na(tx_pvalueStageR))) %>%
dplyr::select(tx_id, gene_name, gene_id, l2fc, tx_pvalueStageR, nom_pval, tx_biotype) %>%
dplyr::arrange(abs(l2fc))
final_repl_drim <- df_repl$drim %>% dplyr::filter(!(is.na(tx_pvalueStageR))) %>%
dplyr::select(tx_id, gene_id, gene_name, l2fc, tx_pvalueStageR, nom_pval, tx_biotype) %>%
dplyr::arrange(abs(l2fc))
final_repl_dexdrim <- dplyr::bind_rows("DRIMSeq" = final_repl_drim, "DEXSeq" = final_repl_dex, .id = "Tool")Both workflows, DRIMSeq and DEXSeq use a collection of transcripts that is created with and filtered by DRIMSeq.
DRIMSeq’s filter function is applied to the scaled transcript counts that result from tximport (scaledTPM).
This is an extract of the filter function description by DRIMSeq:
" Filtering parameters should be adjusted according to the sample size of the experiment data and the number of replicates per condition.
* min_samps_gene_expr defines the minimal number of samples where genes are required to be expressed at the minimal level of min_gene_expr in order to be included in the downstream analysis.
Ideally, we would like that genes were expressed at some minimal level in all samples because this would lead to better estimates of feature ratios. (We defined this parameter to be equal to the number of samples).
* Similarly, min_samps_feature_expr and min_samps_feature_prop defines the minimal number of samples where features are required to be expressed at the minimal levels of counts min_feature_expr or proportions min_feature_prop.
* In differential transcript/exon usage analysis, we suggest using min_samps_feature_expr and min_samps_feature_prop equal to the minimal number of replicates in any of the conditions. (defined as n.small in our case, representing the number of samples of the smaller group (condition).
* For example, in an assay with 3 versus 5 replicates, we would set
these parameters to 3, which allows a situation where a feature is expressed in one condition but
may not be expressed at all in another one, which is an example of differential transcript/exon usage "
## [1] "Filter parameters discovery cohort:"
## n.small n min_feature_expr min_feature_prop
## 11.0 28.0 10.0 0.1
## min_gene_expr
## 10.0
## [1] "Filter parameters replication cohort:"
## n.small n min_feature_expr min_feature_prop
## 10.0 21.0 10.0 0.1
## min_gene_expr
## 10.0
Here I generate two dataframes from the tool data objects to extract counts (after scaling with scaledTPM). We use the counts in CPM to calculate rowwise means and medians to see differences of expression distribution before and after filtering.
# calculated CPMs from counts for comparison of expression. CPMs were calculated with a librarysize per sample based on all transcripts, i.e. before filtering
gene_info <- DTU::get_gene_info(DRIMSeq::counts(obj$Ds_unfilt$Ds_drim_unfilt$discovery)$feature_id, tx = TRUE) %>%
dplyr::select(tx_biotype, tx_id)
# discovery cohort
CPMs <- DRIMSeq::counts(obj$Ds_unfilt$Ds_drim_unfilt$discovery) %>%
dplyr::rename(tx_id = feature_id) %>%
# comment next line to get median expression on count scale (median(CPMs[,-c(1,2)] %>% rowMeans()))
dplyr::mutate_at(grep("\\.", colnames(.)), ~. / sum(.) * 1000000)
CPMs_filtered <- CPMs %>% dplyr::filter(tx_id %in% DRIMSeq::counts(obj$Ds$Ds_drim$discovery)$feature_id)
after <- left_join(CPMs_filtered, gene_info, by = "tx_id") %>%
mutate(rowMeans = rowMeans(.[grep("\\.", names(.))])) %>%
group_by(gene_id) %>% mutate(ntx = n()) %>%
dplyr::select(gene_id, tx_id, tx_biotype, rowMeans, ntx)
before <- left_join(CPMs, gene_info, by = "tx_id") %>%
mutate(rowMeans = rowMeans(.[grep("\\.", names(.))])) %>%
group_by(gene_id) %>% mutate(ntx = n()) %>%
dplyr::select(gene_id, tx_id, tx_biotype, rowMeans, ntx)
df <- gdata::combine(before, after) %>% dplyr::rename(Filter=source)
biotypeCount <- df %>% dplyr::group_by(Filter) %>%
dplyr::count(tx_biotype) %>%
mutate(sum=sum(n),frac = n / sum(n))
ntxInfo <- df %>% dplyr::group_by(Filter) %>%
dplyr::distinct(gene_id,.keep_all = T)
dplyr::group_by(df,Filter) %>% dplyr::summarise(median(rowMeans),sd(rowMeans))## # A tibble: 2 x 3
## Filter `median(rowMeans)` `sd(rowMeans)`
## <fct> <dbl> <dbl>
## 1 before 0.432 871.
## 2 after 1.79 12.4
p1 <- ggplot(df, aes(x = log10(rowMeans), col = Filter)) +
geom_histogram(aes(y = ..density.., fill = Filter), alpha = 0.4, bins = 100) +
geom_density(size = 1.1) +
scale_x_continuous(name = "log10(mean CPM)", limits = c(-8,10)) +
theme_bw() +
scale_color_manual(values = c("deepskyblue3", "darkblue"))+
scale_fill_manual(values = c("deepskyblue3", "darkblue"))+
labs(title = "a")
p2 <- ggplot(ntxInfo, aes(x = Filter, y = log10(ntx))) +
geom_violin(scale = "count", aes(fill = Filter)) +
geom_jitter(width = 0.1, size = 0.3, alpha = 0.01) +
theme_bw() +
scale_y_continuous(name = "log10(# transcripts per gene)") +
labs(x = "", title = "b") +
scale_color_manual(values = c("deepskyblue3", "darkblue"))+
scale_fill_manual(values = c("deepskyblue3", "darkblue"))
p3 <- ggplot(subset(biotypeCount, frac >= 0.001), aes(x = as.factor(tx_biotype), y = frac, fill = Filter)) +
geom_bar( stat = "identity") +
coord_flip() +
facet_wrap(.~Filter) +
theme_bw() +
theme(axis.text.x = element_text(angle = -90)) +
labs(x = "Transcript biotype (Ensembl v75)", y = "Frequency", title = "c") +
scale_color_manual(values = c("deepskyblue3", "darkblue"))+
scale_fill_manual(values = c("deepskyblue3", "darkblue"))+
theme(panel.spacing = unit(1, "lines")) +
theme(strip.background = element_rect(fill = "black"))+
theme(strip.text = element_text(color = "white", face = "bold"))
grid.arrange(p1, p2, p3)## png
## 2
Volcano and MA plots
# generate dataframe with expression counts for plotting
# DRIMSeq
exprMixed_drim <- DRIMSeq::counts(obj$Ds$Ds_drim$discovery) %>%
dplyr::mutate(meanExpr = rowMeans(as.matrix(.[grep('\\.', names(.))]))) %>%
dplyr::select(feature_id, meanExpr) %>% dplyr::rename(tx_id = feature_id)
# join the general discovery DRIMSeq dataframe that we generated at the start,
# with the expression dataframe to have all data in one (pvalues and expression)
df_drimTxLevel <- left_join(df_disc$drim, exprMixed_drim, by = "tx_id") %>%
dplyr::rename(rankOtherTool = rankDex)
# get the gene-level p-values for DRIMSeq
geneLevel_drim <- as.data.frame(DRIMSeq::results(obj$Ds$Ds_drim$discovery)) %>%
dplyr::select(gene_id, pvalue) %>% dplyr::rename(qvalue = pvalue)
# group dataframe by gene_id and calculate how many transcripts each gene has,
# then only keep one (randomly chosen) transcript per gene, so we keep only the gene information
df_drim <- df_drimTxLevel %>% dplyr::group_by(gene_id) %>%
dplyr::mutate(ntx=n()) %>% dplyr::distinct(gene_id, .keep_all = TRUE)
# and join with the dataframe above
df_drim <- left_join(df_drim, geneLevel_drim, by = "gene_id")
# DEXSeq
# extract count data from DEXSeq using their accesor function and modify the tx_id column (original column is a concat of featureID and groupID)
tx_id <- as.data.frame(stringr::str_split(rownames(DEXSeq::featureCounts(obj$Ds$Ds_dex$discovery)), ":", simplify = TRUE))[, 2]
exprMixed_dex <- as.data.frame(DEXSeq::featureCounts(obj$Ds$Ds_dex$discovery)) %>%
dplyr::mutate(meanExpr = rowMeans(.)) %>%
dplyr::select(meanExpr)
exprMixed_dex$tx_id <- tx_id
# join the expression data with the general dataset we generated at the start
df_dexTxLevel <- left_join(df_disc$dex, exprMixed_dex, by="tx_id") %>%
dplyr::rename(rankOtherTool= rankDrim)
#get the gene-level results
geneLevel_dex <- DEXSeq::perGeneQValue(DEXSeq::DEXSeqResults(obj$Ds$Ds_dex$discovery, independentFiltering = FALSE))
geneLevel_dex <- data.frame(gene_id = names(geneLevel_dex), qvalue = geneLevel_dex)
#count number of transcripts per gene
df_dex <- df_dexTxLevel %>% dplyr::group_by(gene_id) %>% dplyr::mutate(ntx = n())
#keep only one (randomly chosen) transcript per gene, as we only need gene info for further plotting
df_dex <- df_dex %>% dplyr::distinct(gene_id,.keep_all = TRUE)
#joing gene-level result with df above
df_dex <- dplyr::left_join(df_dex, geneLevel_dex, by = "gene_id")
#bind rows of both dataframes together
dfGeneLevel <- gdata::combine(df_drim, df_dex, names = c("DRIMSeq","DEXSeq")) %>%
dplyr::rename(tool = source)
dfTxLevel <- gdata::combine(df_drimTxLevel, df_dexTxLevel, names = c("DRIMSeq","DEXSeq")) %>%
dplyr::rename(tool = source)
plotVolcano <- function(df,alpha=0.05,title=""){
df$sig<-sapply(seq(1,nrow(df)),function(i)(ifelse(df[i,"nom_pval"]<0.05,"TRUE","FALSE")))
# the following lines mark the extreme DEXSeq p-value outliers such that they can be seen in the plot
df %<>% dplyr::mutate(outlier=ifelse(-log10(nom_pval)>10,TRUE,FALSE),nom_pval=ifelse(-log10(nom_pval)>10,10^-11,nom_pval))
ggplot(df) +
geom_point(aes(x=l2fc,y=-log10(nom_pval),col=as.factor(sig),shape=outlier),alpha=0.3,show.legend=F) +
geom_hline(yintercept=0) +
scale_color_manual(labels=c("TRUE"="p-value < 0.05","FALSE" = "not signif."),values=c("TRUE"="red","FALSE"="grey")) +
labs(y="-log10(p-value)",x="effect size",col="Significance",tag=title) +
facet_wrap(~tool)+#,scales="free_y") +
#coord_fixed() +
geom_vline(xintercept=-0.1,col="grey39") +
geom_vline(xintercept=.1,col="grey39") +
geom_hline(yintercept=-log10(alpha),col="darkblue",lty="dotted") +
theme_bw() +
theme(plot.title = element_text(hjust = 0.5)) +
theme(strip.background=element_rect(fill="black")) +
theme(strip.text= element_text(color="white",face="bold"))
}
my_plotMA <- function(df,alpha=0.05,title=""){
df$sig<-sapply(seq(1,nrow(df)),function(i)(ifelse(df[i,"nom_pval"]<0.05,"TRUE","FALSE")))
df %<>% dplyr::mutate(outlier=ifelse(abs(l2fc)>3,TRUE,FALSE),l2fc=ifelse(abs(l2fc)>3,3.2,l2fc))
ggplot(df, aes(x=log10(meanExpr),y=l2fc,col=as.factor(sig))) +
geom_point(alpha=0.3,aes(shape=outlier)) +
facet_wrap(~tool) +
scale_color_manual(labels=c("TRUE"="p-value < 0.05","FALSE" = "not signif."),values=c("TRUE"="red","FALSE"="grey")) +
labs(x="log10(mean expression)",y="Effect size",col="Significance",tag=title) +
theme_bw() +
theme(plot.title = element_text(hjust = 0.5)) +
theme(strip.background=element_rect(fill="black")) +
theme(strip.text= element_text(color="white",face="bold")) +
theme(legend.position="bottom",plot.tag = element_text(margin = margin(t=0))) +
theme(plot.margin=unit(c(0,0,0,0),"mm"))
}
plot_pvalDist<-function(df,tag) {
df %>% dplyr::mutate(ntxLabel=paste0(ntx," transcripts/gene")) %>%
ggplot(.,aes(x=qvalue,y=..density..)) +
geom_histogram(aes(fill=tool),col="black") +
geom_density() +
facet_grid(rows=vars(ntxLabel),cols=vars(tool),scales="free") +
scale_fill_manual(values=c("DEXSeq"=colorFriendly[["blue"]],"DRIMSeq"=colorFriendly[["orange"]]))+
theme_bw() +
theme(plot.title = element_text(hjust = 0.5)) +
theme(strip.background=element_rect(fill="black")) +
theme(strip.text= element_text(color="white",face="bold")) +
labs(tag=tag,fill="Tool",x="gene-level p-value",y="density")
}
p1 <- plotVolcano(dfTxLevel,title="a")
p2 <- my_plotMA(dfTxLevel,title="b")
p3 <- plot_pvalDist(dfGeneLevel,tag="c")
(p1/p2 + plot_layout(heights=c(1,2))) | p3 svg(paste0(plotOutDir,"S1.svg"),width=13,height=10)
(p1/p2 + plot_layout(heights=c(1,2))) | p3
dev.off()## png
## 2
Comparing effect size of DRIMSeq and DEXseq.
Effect size refers to the coefficient of the model of the respective tool, which was assigned to the variable “condition”, i.e. CT vs PD.
For the effect size of DRIMSeq we applied a transformation: log2(exp(effectSize)).
# Correlations mentioned in the manuscript
# DTU events of either tool
ids <- unique(c(final_disc_drim$tx_id,final_disc_dex$tx_id))
events <- dplyr::left_join(subset(obj$main_df$discovery$dex,tx_id %in% ids),subset(obj$main_df$discovery$drim,tx_id %in% ids),by=c("gene_id","tx_id"))
cor.test(events$l2fc.x,events$l2fc.y)##
## Pearson's product-moment correlation
##
## data: events$l2fc.x and events$l2fc.y
## t = 151.12, df = 812, p-value < 2.2e-16
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
## 0.9801534 0.9848935
## sample estimates:
## cor
## 0.9826835
# How many of the DTU events identified by one method are nom. sig in the alternative method
# Number of DEXSeq DTU events
a <- nrow(final_disc_dex)
b <- nrow(subset(obj$main_df$discovery$drim, tx_id %in% final_disc_dex$tx_id & nom_pval < 0.05))
(b / a) * 100## [1] 97.94118
# Number of DRIMSeq DTU events
a <- nrow(final_disc_drim)
b <- nrow(subset(obj$main_df$discovery$dex, tx_id %in% final_disc_drim$tx_id & nom_pval < 0.05))
(b / a) * 100## [1] 97.20588
# dfs that contain all info
drim <- obj$main_df$discovery$drim
dex <- obj$main_df$discovery$dex
dfList <- make_df(drim,dex)
p1 <- makeplot(dfList[[1]], tag = "a", legend = "none")
p2 <- makeplot(dfList[[2]], tag = "b", legend = "bottom")
p3 <- makeplot(dfList[[3]], tag = "c", legend = "none")
p4 <- makeplot(dfList[[4]], tag = "d", legend = "none")
combined <- (p1 | p2) / (p3 | p4) #& theme(legend.position = "bottom")
combinedsvg(paste0(plotOutDir,"Figure4.svg"),width=10,height=10)
combined / guide_area() + plot_layout(guides = "collect",widths=c(3,1))
dev.off() ## png
## 2
For the replication cohort(Fig. S2):
#prepare the dfs that contain all info
drim <- obj$main_df$replication$drim
dex <- obj$main_df$replication$dex
dfList <- make_df(drim,dex)
p1 <- makeplot(dfList[[1]], tag = "a", legend = "none")
p2 <- makeplot(dfList[[2]], tag = "b", legend = "bottom")
p3 <- makeplot(dfList[[3]], tag = "c", legend = "none")
p4 <- makeplot(dfList[[4]],tag = "d", legend = "none")
combined <- (p1 | p2) / (p3 | p4)
combinedsvg(paste0(plotOutDir,"S2.svg"), width = 10, height = 10)
combined / guide_area() + plot_layout(guides = "collect", widths = c(3,1))
dev.off() ## png
## 2
## [1] "Number of transcripts in both cohorts"
## [1] 29807
Agreement on effect size across cohorts (Fig.6)
#plot correlation
cor <- T
# create replication cohort df's which contain all transcripts that are in the final discovery cohort list created at the beginning
final_repl_dex <- df_repl$dex %>% dplyr::filter(tx_id %in% final_disc_dex$tx_id) %>% dplyr::select(tx_id,gene_id,l2fc,nom_pval)
final_repl_drim <- df_repl$drim %>% dplyr::filter(tx_id %in% final_disc_drim$tx_id) %>% dplyr::select(tx_id ,gene_id,l2fc,nom_pval)
# join cohort dataframes for each tool
# DEXSeq
dfDex <- na.omit(left_join(final_disc_dex,final_repl_dex, by = "tx_id", suffix = c("_disc","_repl")))
# helper coloumn for plottig, whether or not transcript is nominally significant in repl. cohort according to DEXSeq
dfDex$sigRepl <- sapply(dfDex$nom_pval_repl, function(i)(ifelse(i < 0.05, 1, 0)))
dfDex$label <- sapply(dfDex$gene_name, function(g)(ifelse(g %in% c("ZNF189"), as.character(g), "")))
# Do the same for DRIMSeq
dfDrim <- na.omit(left_join(final_disc_drim, final_repl_drim, by = "tx_id", suffix = c("_disc","_repl")))
dfDrim$sigRepl <- sapply(dfDrim$nom_pval_repl, function(i)(ifelse(i < 0.05, 1, 0)))
dfDrim$label <- sapply(dfDrim$gene_name, function(g)(ifelse(g %in% "ZNF189", as.character(g), "")))
#only one transcript of the lab genes is significant after stageR,
#thats why we see only one point for each of the two genes in the plot
agreementPlot <- function(df,tag="",legend="none") {
ggplot(data=df,aes(x=l2fc_repl,y=l2fc_disc)) +
geom_point(aes(col=as.factor(sigRepl)),alpha=.3) +
stat_density2d(col="black",size=0.3) +
geom_abline(intercept = 0, slope = 1,lty="dashed",) +
labs(title="",tag=tag,x="effect size replication cohort",y="effect size discovery cohort",col="Nominal p-value (replication cohort)") +
scale_color_manual(values=c("1"="red","0"="black"),labels=c("1"="<0.05","0"=">0.05")) +
facet_wrap(~Tool) + #,scales="free") +
scale_fill_manual(values=c("1"="red","0"="grey")) +
geom_hline(aes(yintercept=0),col="grey") +
geom_vline(aes(xintercept=0),col="grey") +
scale_x_continuous(limits=c(-max(c(abs(df$l2fc_repl),abs(df$l2fc_disc))),max(c(abs(df$l2fc_repl),abs(df$l2fc_disc))))) +
scale_y_continuous(limits=c(-max(c(abs(df$l2fc_repl),abs(df$l2fc_disc))),max(c(abs(df$l2fc_repl),abs(df$l2fc_disc)))) )+
coord_fixed() +
# geom_label_repel(aes(label=label)) +
theme_bw() +
theme(plot.title = element_text(hjust = 0.5)) +
theme(panel.spacing = unit(1, "lines")) +
theme(strip.background=element_rect(fill="black"))+
theme(strip.text= element_text(color="white",face="bold")) +
guides(fill = FALSE, size = FALSE) +
theme(legend.position = legend)
}
df <- dfDex %>% dplyr::bind_rows("DEXSeq" = ., "DRIMSeq" = dfDrim, .id = "Tool")
nrow(dfDrim)## [1] 481
## [1] 0.3573096
##
## Pearson's product-moment correlation
##
## data: sign(dfDrim$l2fc_repl) and sign(dfDrim$l2fc_disc)
## t = 6.4678, df = 479, p-value = 2.457e-10
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
## 0.1990432 0.3636012
## sample estimates:
## cor
## 0.283407
## [1] "percent agreement dex"
## [1] "62.83"
## [1] "percent agreement drim"
## [1] "64.24"
#Basically this is the same as above just that this time we do use all transcripts of discovery not only the ones which survived stageR correction
#This is only done for DRIMSeq this time
# define ids which are in both cohorts
ids <- Reduce(intersect,list(df_repl$drim$tx_id,df_disc$drim$tx_id))
# merge ids with replication df
df <- left_join(data.frame(tx_id = ids), df_repl$drim, by = "tx_id", suffix = c("","replication"))
# add discovery df
df <- left_join(df, df_disc$drim, by = "tx_id", suffix = c("_repl","_disc"))
#helper columns for plotting.
#disc repl +(disc sig)(repl sig)(&&) (||)
# 1 -1 0 1 1 1 1
# -1 2 1 0 0 0 0
# 1 2 3 1 0 0 1
# -1 -1 2 0 1 0 1
#TODO: replace with dplyr instead of using sapply
df$sigDisc <- sapply(df$nom_pval_disc, function(i)(ifelse(i < 0.05, 1, -1)))
df$sigRepl <- sapply(df$nom_pval_repl,function(i)(ifelse(i < 0.05, -1, 2)))
df$sigCol <- as.factor(sapply(seq(1, nrow(df)), function(i)(df[i, "sigDisc"] + df[i, "sigRepl"])))
# for plot legend
df$sigColLabel <- plyr::revalue(df$sigCol, c("0" = "Sig. in both cohorts", "1" = "Not sig. in either cohort", "3" = "Sig. in the discovery cohort only", "-2" = "Sig. in the replication cohort only"))
#replace stageR assigned NA value with 1s
df$tx_pvalueStageR_repl <- sapply(df$tx_pvalueStageR_repl, function(i)(ifelse(is.na(i), 1, i)))
df$tx_pvalueStageR_disc <- sapply(df$tx_pvalueStageR_disc, function(i)(ifelse(is.na(i), 1, i)))
#helper col tags transcripts which have the same sign of l2fc (or effect size)
df$agreelfc <- as.factor(sapply(seq(1,nrow(df)),function(i) {
ifelse(sign(df[i, "l2fc_repl"]) == sign(df[i,"l2fc_disc"]),1,0)
}))
print("percentage of tx agreeing on direction disc. cohort not repl. cohort")## [1] "percentage of tx agreeing on direction disc. cohort not repl. cohort"
## [1] "59.3"
## [1] "percentage of tx agreeing on direction disc. cohort and repl. cohort"
## [1] "62.37"
## [1] "percentage of tx agreeing on direction repl. cohort not disc. cohort"
## [1] "52.91"
#effect size agreement plot
esa_plot <- ggplot(data=df,aes(x=l2fc_repl,y=l2fc_disc)) +
geom_point(aes(col=as.numeric(tx_pvalueStageR_disc)),alpha=0.5) +
stat_density2d(col="black",size=0.2)+
facet_wrap(~sigColLabel) + scale_fill_viridis_c() +
coord_fixed() +
scale_color_gradient(low="red",high="grey") +
geom_abline(intercept = 0, slope = 1,lty="dashed",) +
labs(title="",x="effect size replication cohort",y="effect size discovery cohort",fill="",col="Adj. p-value (discovery cohort)",tag="a") +
geom_hline(aes(yintercept=0),col="grey") +
geom_vline(aes(xintercept=0),col="grey") +
theme_bw() +
theme(plot.title = element_text(hjust = 0.5)) +
theme(panel.spacing = unit(1, "lines")) +
theme(strip.background=element_rect(fill="black"))+
theme(strip.text= element_text(color="white",face="bold")) +
guides(alpha = FALSE, size = FALSE) +
theme(legend.position="right")
if (cor == TRUE){
esa_plot <- esa_plot +
stat_cor()
p <- p +
stat_cor()
}
svg(paste0(plotOutDir,"Figure6.svg"),width=12,height=12)
esa_plot / p + plot_layout(widths=c(1.5,1))
dev.off()## png
## 2
Agreement on direction of effect size (run previous chunk to create df used here)
#df %<>% dplyr::filter(!(is.na(gene_id_repl)))
# not sig in either cohort
nonSig <- subset(df, sigCol == 1)
nrow(nonSig)## [1] 25002
## 1
## 0.5354372
## [1] 29807
##
## Pearson's product-moment correlation
##
## data: sign(nonSig$l2fc_disc) and sign(nonSig$l2fc_repl)
## t = 11.221, df = 25000, p-value < 2.2e-16
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
## 0.05844659 0.08311340
## sample estimates:
## cor
## 0.07079081
## [1] 3776
##
## Pearson's product-moment correlation
##
## data: sign(sig$l2fc_disc) and sign(sig$l2fc_repl)
## t = 11.946, df = 3774, p-value < 2.2e-16
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
## 0.1599510 0.2214241
## sample estimates:
## cor
## 0.1908747
## [1] 186
##
## Pearson's product-moment correlation
##
## data: sign(sig$l2fc_disc) and sign(sig$l2fc_repl)
## t = 3.4838, df = 184, p-value = 0.0006178
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
## 0.1087676 0.3790664
## sample estimates:
## cor
## 0.2487541
## [1] 843
##
## Pearson's product-moment correlation
##
## data: sign(sig$l2fc_disc) and sign(sig$l2fc_repl)
## t = 1.685, df = 841, p-value = 0.09235
## alternative hypothesis: true correlation is not equal to 0
## 95 percent confidence interval:
## -0.009553114 0.125039125
## sample estimates:
## cor
## 0.05800659
Number of genes with a significant pvalue after stageR
## [1] "DEXSeq"
## [1] 254
## [1] "DRIMSeq"
## [1] 495
## [1] "all genes"
## [1] 584
## [1] 814
## [1] "tool int"
## [1] 165
How many transcrips of which transcript biotype were significant
## [1] "DRIMSeq"
##
## antisense lincRNA
## 15 22
## nonsense_mediated_decay processed_pseudogene
## 18 4
## processed_transcript protein_coding
## 94 455
## retained_intron transcribed_unprocessed_pseudogene
## 70 2
## [1] "DEXSeq"
##
## antisense lincRNA nonsense_mediated_decay
## 5 5 14
## processed_transcript protein_coding retained_intron
## 58 208 50
How many transcrips per gene
## [1] "DRIMSeq"
##
## 1 2 3
## 312 181 2
## [1] "DEXSeq"
##
## 1 2 3
## 173 76 5
Number of missing genes in replication due to low expression
## [1] "DEXSeq"
dexN <- nrow(left_join(final_disc_dex,df_repl$dex[,c("tx_id","nom_pval","l2fc")],by="tx_id") %>% dplyr::distinct(gene_id,.keep_all=T))
NmissingDexRepl <- colSums(is.na(left_join(final_disc_dex,df_repl$dex[,c("tx_id","nom_pval","l2fc")],by="tx_id") %>% dplyr::distinct(gene_id,.keep_all=T)))
print(NmissingDexRepl["l2fc.y"])## l2fc.y
## 83
## tx_id gene_name gene_id l2fc.x
## 254 254 254 254
## tx_pvalueStageR nom_pval.x tx_biotype nom_pval.y
## 254 254 254 171
## l2fc.y
## 171
## [1] "DRIMSeq"
drimN <- nrow(left_join(final_disc_drim,df_repl$drim[,c("tx_id","nom_pval","l2fc")],by="tx_id") %>% dplyr::distinct(gene_id,.keep_all=T))
NmissingDrimRepl <- colSums(is.na(left_join(final_disc_drim,df_repl$drim[,c("tx_id","nom_pval","l2fc")],by="tx_id") %>% dplyr::distinct(gene_id,.keep_all=T)))
print(NmissingDrimRepl["l2fc.y"])## l2fc.y
## 130
## tx_id gene_id gene_name l2fc.x
## 495 495 495 495
## tx_pvalueStageR nom_pval.x tx_biotype nom_pval.y
## 495 495 495 365
## l2fc.y
## 365
Format function for latex:
myFormat <- function(val){
nVal=as.character(round(val,digits=2))
for(i in 1:length(nVal)){
if(sign(val[i])==1 | sign(val[i])==0) # if is pos
{
nVal[i]=paste0("\\ ",nVal[i])
}
if(nVal[i] == "\\ 0")
{
nVal[i] <- "\\ 0.00"
}
}
return(nVal)
}Latex tables
#DEXSeq
#exclue all transcripts which are not present in replication (NA's)
df <- na.omit(left_join(final_disc_dex,obj$main_df$replication$dex[,c("tx_id", "nom_pval", "l2fc")], by = "tx_id", suffix = c("_disc", "_repl")))
# retain only transcripts where the sign of the l2fc or effect size in discovery equals the sign in replication
df <- df %>% dplyr::filter(sign(l2fc_disc) == sign(l2fc_repl), nom_pval_repl < 0.05)
#format for latex and sort by discovery transcript stageR pvalue
df %<>% dplyr::select(gene_name, tx_id, tx_biotype, tx_pvalueStageR, l2fc_disc, l2fc_repl) %>%
dplyr::arrange(tx_pvalueStageR) %>%
dplyr::mutate_at(3,~gsub("_"," ",.)) %>%
dplyr::mutate_at(4:6,~myFormat(.)) %>% #~formatC(.,digit=3,format="E",flag=" ")) %>%
dplyr::mutate_at(2:6,~paste0("&",.)) %>%
dplyr::mutate_at(6,~paste0(.,"\\\\")) %>%
dplyr::select(-(tx_pvalueStageR)) %>%
tibble::add_column(.,tool=rep("&DEXSeq&",nrow(.)),.before=1)
write.table(df,file=paste0(tableOutDir,"dexFinal.txt"),quote=F,col.names=F,row.names=F)
#DRIMSeq
#the same as above
df <- na.omit(left_join(final_disc_drim,obj$main_df$replication$drim[,c("tx_id","nom_pval","l2fc")],by="tx_id",suffix=c("_disc","_replication")))
df <- df %>% dplyr::filter(sign(l2fc_disc) == sign(l2fc_replication), nom_pval_replication < 0.05)
#compare to dge results of discovery
df <- dplyr::left_join(df,obj$dge_results$discovery, by = "gene_id")
#number of DTU genes picked up by DGE:
df %>% dplyr::filter(padj < 0.05)## tx_id gene_id gene_name l2fc_disc tx_pvalueStageR
## 1 ENST00000334029 ENSG00000100033 PRODH -1.479819 0.003288
## 2 ENST00000264381 ENSG00000114200 BCHE -1.814029 0.000000
## 3 ENST00000540653 ENSG00000114200 BCHE 1.814029 0.000000
## nom_pval_disc tx_biotype nom_pval_replication l2fc_replication
## 1 4.586449e-05 protein_coding 0.01234035 -1.392379
## 2 1.976966e-04 protein_coding 0.03510185 -1.063644
## 3 1.976966e-04 protein_coding 0.03510185 1.063644
## baseMean log2FoldChange lfcSE stat pvalue padj
## 1 1761.1068 -1.1671971 0.2646551 -4.410258 1.032475e-05 0.01093284
## 2 186.5362 -0.9567699 0.2313975 -4.134746 3.553482e-05 0.01621397
## 3 186.5362 -0.9567699 0.2313975 -4.134746 3.553482e-05 0.01621397
## length(unique(gene_id))
## 1 17
#format for latex and sort by discovery transcript stageR pvalue
df %<>% dplyr::select(gene_name, tx_id, tx_biotype, tx_pvalueStageR, l2fc_disc, l2fc_replication) %>%
dplyr::arrange(tx_pvalueStageR) %>%
dplyr::mutate_at(3,~gsub("_"," ",.)) %>%
dplyr::mutate_at(4:6,~myFormat(.)) %>% #~formatC(.,digit=3,format="E",flag=" ")) %>%
dplyr::mutate_at(2:6,~paste0("&",.)) %>%
dplyr::mutate_at(6,~paste0(.,"\\\\")) %>%
dplyr::select(-(tx_pvalueStageR)) %>%
tibble::add_column(.,tool=rep("&DRIMSeq&",nrow(.)),.before=1)
# uncomment
# write.table(df,file=paste0(tableOutDir,"drimFinal.txt"),quote=F,col.names=F,row.names=F)These plots are not included in the paper but nice to have for a quick look.
#DRIMSeq
#the same as above
df_drim <- na.omit(left_join(final_disc_drim,obj$main_df$replication$drim[,c("tx_id", "nom_pval","l2fc")],by="tx_id",suffix=c("_disc","_repl"))) %>%
dplyr::filter(sign(l2fc_disc) == sign(l2fc_repl), nom_pval_repl < 0.05)
#
#DEXSeq
#exclue all transcripts which are not present in replication (NA's)
df_dex <- na.omit(left_join(final_disc_dex, obj$main_df$replication$dex[, c("tx_id", "nom_pval", "l2fc")], by = "tx_id", suffix = c("_disc","_repl"))) %>%
dplyr::filter(sign(l2fc_disc) == sign(l2fc_repl), nom_pval_repl < 0.05)
#plot all replicated DTU genes of DRIMSeq
genes_to_plot <- DTU::get_gene_info(unique(df_drim$tx_id,df_dex), tx = T)
# Generate count plots and count dfs for both cohorts for those transcripts
# This is an annoying problem: Within DRIMSeq (e.g. when calling counts), sample_ids get changed
# Probably somewhere in as.data.frame where check.names==T
# hyphens become dots (Ctr-1 -> Ctr.1)
# dirty quick fix (not necessary for DEXSeq)
new_obj <- obj
new_obj$info <- lapply (obj$info, function (i) {
i %<>% dplyr::mutate(sample_id = gsub("-",".",sample_id))
})
new_obj$dge <- lapply(new_obj$dge, function (o) {
snames <- gsub("-",".",colnames(o))
SummarizedExperiment::colData(o) %<>% as.data.frame() %>%
dplyr::mutate(sample_id = snames, sample_id1 = snames,
sample_id2 = snames) %>%
DataFrame()
colnames(o) <- snames
return(o)
})
plots <- DTU::plot_genes_cohort(genes_toplot = genes_to_plot ,
tool = "drim",
only_nom_sig = F,
conditions = c("CT","PD"),
out = plotOutDir,
obj = new_obj,
cohort = "discovery",
selected_samples = NULL,
want_jitter = F)## [1] "extracting counts from the provided count object assuming it is a drim object"
SNCA,PARK2,PARK7,GBA,PINK1,SRRM2,GBA,FBXO7,LRRK2
## tx_id gene_pvalueStageR tx_pvalueStageR nom_pval toolAdjPval
## 1 ENST00000506244 NA NA 0.0553810 0.3879063
## 2 ENST00000394991 NA NA 0.2001971 0.6406055
## 3 ENST00000394989 NA NA 1.0000000 1.0000000
## 4 ENST00000336904 NA NA 1.0000000 1.0000000
## gene_id gene_name tx_biotype l2fc rankDex
## 1 ENSG00000145335 SNCA protein_coding -0.48521625 7988
## 2 ENSG00000145335 SNCA protein_coding 0.39047771 7870
## 3 ENSG00000145335 SNCA protein_coding 0.03641492 36731
## 4 ENSG00000145335 SNCA protein_coding 0.07639267 35458
## tx_id gene_pvalueStageR tx_pvalueStageR nom_pval toolAdjPval
## 1 ENST00000394991 NA NA 0.07418454 0.3819514
## 2 ENST00000506244 NA NA 0.07617850 0.3860695
## 3 ENST00000336904 NA NA 0.82509968 0.9428913
## 4 ENST00000394989 NA NA 0.86948859 0.9591693
## gene_id gene_name tx_biotype l2fc rankDrim
## 1 ENSG00000145335 SNCA protein_coding 0.36728038 12663
## 2 ENSG00000145335 SNCA protein_coding -0.57280076 5785
## 3 ENSG00000145335 SNCA protein_coding 0.08534661 39040
## 4 ENSG00000145335 SNCA protein_coding 0.06685536 39039
## [1] tx_id gene_pvalueStageR tx_pvalueStageR
## [4] nom_pval toolAdjPval gene_id
## [7] gene_name tx_biotype l2fc
## [10] rankDex
## <0 rows> (or 0-length row.names)
## [1] tx_id gene_pvalueStageR tx_pvalueStageR
## [4] nom_pval toolAdjPval gene_id
## [7] gene_name tx_biotype l2fc
## [10] rankDrim
## <0 rows> (or 0-length row.names)
## tx_id gene_pvalueStageR tx_pvalueStageR nom_pval toolAdjPval
## 1 ENST00000366898 NA NA 0.7949749 0.947643
## 2 ENST00000366892 NA NA 0.7949749 0.947643
## gene_id gene_name tx_biotype l2fc rankDex
## 1 ENSG00000185345 PARK2 protein_coding 0.08697873 37508
## 2 ENSG00000185345 PARK2 protein_coding -0.08697873 37563
## tx_id gene_pvalueStageR tx_pvalueStageR nom_pval toolAdjPval
## 1 ENST00000366898 NA NA 0.8976597 0.9697126
## 2 ENST00000366892 NA NA 0.8995228 0.9703191
## gene_id gene_name tx_biotype l2fc rankDrim
## 1 ENSG00000185345 PARK2 protein_coding 0.04684074 33986
## 2 ENSG00000185345 PARK2 protein_coding -0.04726718 33987
For this we use the result dataframe of the differential gene expression analysis.
DGE <- subset(obj$dge_results$discovery, padj < 0.05)
a <- length(unique(c(final_disc_drim$gene_id,final_disc_dex$gene_id)))
b <- sum(unique(c(final_disc_drim$gene_id,final_disc_dex$gene_id)) %in% DGE$gene_id)
(b / a) * 100## [1] 2.226027
#for each tool, subset the df to contain only dtu events of genes which appear in the DGE df
drimReprod <- final_disc_drim %>% dplyr::filter(gene_id %in% DGE$gene_id)
dexReprod <- final_disc_dex %>% dplyr::filter(gene_id %in% DGE$gene_id)
bothToolReprod <- final_disc_dexdrim %>% dplyr::filter(gene_id %in% DGE$gene_id)
#compare effect size for these candidates
df <- dplyr::left_join(bothToolReprod, DGE, by = "gene_id") %>%
dplyr::group_by(gene_id) %>%
dplyr::select(Tool, tx_id, gene_id, gene_name, l2fc, tx_biotype, log2FoldChange) %>%
dplyr::ungroup()
df %<>% dplyr::select(Tool, gene_name, tx_id, tx_biotype, l2fc, log2FoldChange) %>%
dplyr::arrange(gene_name) %>%
dplyr::mutate_at(4, ~gsub("_"," ",.)) %>%
dplyr::mutate_at(5:6, ~myFormat(.)) %>%
dplyr::mutate_at(2:6, ~paste0("&",.)) %>%
dplyr::mutate_at(6, ~paste0(.,"\\\\"))
# uncomment
# write.table(df,file=paste0(tableOutDir,"DGEDTU.txt"),quote=F,col.names=F,row.names=F)DGE <- subset(obj$dge_results$discovery, padj < 0.05)
df <- final_disc_dexdrim
df %<>% dplyr::group_by(Tool) %>%
dplyr::count(tx_biotype) %>%
mutate(sum = sum(n), frac = 100 * (n / sum(n)))%>%
mutate(tx_biotype = ifelse(tx_biotype == "transcribed_unprocessed_pseudogene", paste0("transcribed_processed","\n","pseudogene"),tx_biotype))
resultPlotBiotype <- ggplot(data = df, aes(x = tx_biotype, fill = Tool)) +
geom_bar(aes(y = frac), stat = "identity") +
scale_fill_manual(values = c("DEXSeq" = colorFriendly[["blue"]],
"DRIMSeq" = colorFriendly[["orange"]])) +
facet_wrap(~Tool, scales = "free") +
theme_bw() +
coord_flip() +
#theme(axis.text.x = element_text(angle = 45)) +
labs(x = "Transcript biotype (Ensembl v75)", y = "Frequency (%)", tag = "b", fill = "") +
theme(panel.spacing = unit(1, "lines")) +
theme(strip.background = element_rect(fill = "black"))+
theme(legend.position = "none")+
theme(strip.text = element_text(color = "white", face = "bold"))
drim <- unique(final_disc_drim$gene_id)
dex <- unique(final_disc_dex$gene_id)
n12=length(Reduce(intersect,list(dex,drim)))
n13=length(Reduce(intersect,list(dex,DGE$gene_id)))
n23=length(Reduce(intersect,list(drim,DGE$gene_id)))
n123=length(Reduce(intersect,list(drim,dex,DGE$gene_id)))
venn<-draw.triple.venn(ind=F, cat.fontfamily = "sans", fontfamilyi = "sans", area1 = length(dex), area2 = length(drim), area3 = length(DGE$gene_id), n12 = n12, n13 = n13, n23 = n23, n123 = n123, category = c("DEXSeq", "DRIMSeq", "DGE"), fill = c(colorFriendly["blue"], colorFriendly["orange"], colorFriendly["green"]), ext.text = TRUE, label.col = "white", alpha = .7,cat.dist=c(.1,.1,.1))
lay<-rbind(c(1,NA,NA,NA),
c(NA,2,2,NA),
c(NA,2,2,NA),
c(3,3,3,3),
c(3,3,3,3),
c(3,3,3,3),
c(3,3,3,3))
grid.arrange(textGrob("a"),gTree(children=venn),resultPlotBiotype,layout_matrix=lay)svg(paste0(plotOutDir,"Figure1.svg"),width=7,height=9)
grid.arrange(textGrob("a"),gTree(children=venn),resultPlotBiotype,layout_matrix=lay)
dev.off()## png
## 2
dge <- dge_results$discovery %>% dplyr::filter(gene_id %in% c(final_disc_drim$gene_id, final_disc_dex$gene_id))
# Join dge with dtu results, i.e. select max(abs(l2fc)) in a gene group
drim <- final_disc_drim %>% dplyr::filter(tx_biotype == "protein_coding")
dex <- final_disc_dex %>% dplyr::filter(tx_biotype == "protein_coding")
df <- dplyr::bind_rows("DRIMSeq" = drim, "DEXSeq" = dex, .id = "Tool")
dge <- dplyr::left_join(df, dge, by = "gene_id", suffix = c("dge", "dtu")) %>%
dplyr::group_by(Tool, gene_id) %>%
dplyr::add_tally() %>%
dplyr::mutate(sig = ifelse(padj < 0.05, 1, 0))
# For the plot of genes with two DTU events
twoTx <- ggplot(subset(dge, n == 2), aes(x = log2FoldChange, y = l2fc, group = gene_id)) +
geom_point(aes(col = padj)) +
geom_line(lwd = 0.5, col = "grey", alpha = .5) +
geom_rug(col=rgb(.5, 0, 0, alpha = .2)) +
facet_wrap(~ Tool) +
labs(x = "Effect size DGE", col = "Adj. p-value DGE", y = "Effect size DTU", tag = "a") +
theme_bw() +
theme(strip.background = element_rect(fill = "black"))+
theme(strip.text = element_text(color = "white", face = "bold")) +
theme(legend.position = "bottom") +
guides(col = "none")
# Plot with genes with one DTU event
OneTx <- ggplot(subset(dge, n == 1), aes(x = log2FoldChange, y = l2fc)) +
geom_point(aes(col = padj)) +
geom_smooth(lwd = 0.5, col = "black") +
stat_cor(method = "pearson") +
geom_rug(col = rgb(.5, 0, 0, alpha = .2)) +
facet_wrap(~ Tool) +
theme_bw() +
theme(strip.background = element_rect(fill = "black"))+
theme(strip.text = element_text(color = "white", face = "bold")) +
theme(legend.position = "bottom") +
labs(x = "Effect size DGE", y = "Effect size DTU", col = "Adj. p-value DGE", tag = "b")
grid.arrange(twoTx,OneTx) ## png
## 2
With STRINGdb and a background comprised of all genes which showed sufficient expression to survive filtering.
(Discovery cohort and DRIMSeq)
# Load stringdb data for homo sapiens
string_db <- STRINGdb$new(species=9606,score_threshold=0,version="10")
# Define hits
hits <- unique(final_disc_dex$gene_name, final_disc_drim$gene_name)
# Define gene background
bg <- unique(df_disc$drim$gene_name, df_disc$dex_gene_name)
# Map gene names to what is needed for stringdb
hits <- string_db$map(data.frame(gene = hits), "gene", removeUnmappedRows = T ) ## Warning: we couldn't map to STRING 5% of your identifiers
## Warning: we couldn't map to STRING 13% of your identifiers
## IGRAPH 9bdd806 UN-- 11026 1713941 --
## + attr: name (v/c), neighborhood (e/n), neighborhood_transferred
## | (e/n), fusion (e/n), cooccurence (e/n), homology (e/n),
## | coexpression (e/n), coexpression_transferred (e/n), experiments
## | (e/n), experiments_transferred (e/n), database (e/n),
## | database_transferred (e/n), textmining (e/n),
## | textmining_transferred (e/n), combined_score (e/n)
## + edges from 9bdd806 (vertex names):
## [1] 9606.ENSP00000003100--9606.ENSP00000008527
## [2] 9606.ENSP00000003100--9606.ENSP00000054666
## [3] 9606.ENSP00000003100--9606.ENSP00000200652
## + ... omitted several edges
# Run enrichment analysis
bp <- string_db$get_enrichment(hits$STRING_id, category = "Process",
methodMT = "fdr", iea = TRUE ) %>%
dplyr::filter(pvalue_fdr < 0.05) %>%
tbl_df
bp %>% kable(.) %>%
kable_styling() %>%
scroll_box(width = "800px", height = "200px")| term_id | proteins | hits | pvalue | pvalue_fdr | term_description |
|---|---|---|---|---|---|
| GO:0050793 | 1112 | 33 | 0.0000000 | 0.0000146 | regulation of developmental process |
| GO:0032879 | 1252 | 35 | 0.0000000 | 0.0000146 | regulation of localization |
| GO:0045595 | 769 | 26 | 0.0000000 | 0.0000245 | regulation of cell differentiation |
| GO:0051094 | 594 | 22 | 0.0000001 | 0.0000500 | positive regulation of developmental process |
| GO:2000026 | 820 | 26 | 0.0000001 | 0.0000527 | regulation of multicellular organismal development |
| GO:0051049 | 944 | 28 | 0.0000001 | 0.0000531 | regulation of transport |
| GO:0035556 | 1071 | 30 | 0.0000001 | 0.0000531 | intracellular signal transduction |
| GO:0051239 | 1216 | 32 | 0.0000002 | 0.0000689 | regulation of multicellular organismal process |
| GO:0051128 | 1278 | 32 | 0.0000005 | 0.0001847 | regulation of cellular component organization |
| GO:0032535 | 169 | 11 | 0.0000007 | 0.0001889 | regulation of cellular component size |
| GO:0002376 | 981 | 27 | 0.0000008 | 0.0001889 | immune system process |
| GO:0007399 | 1172 | 30 | 0.0000008 | 0.0001889 | nervous system development |
| GO:0044711 | 805 | 24 | 0.0000009 | 0.0001889 | single-organism biosynthetic process |
| GO:0033554 | 1048 | 28 | 0.0000009 | 0.0001889 | cellular response to stress |
| GO:0023051 | 1469 | 34 | 0.0000014 | 0.0002620 | regulation of signaling |
| GO:0045428 | 21 | 5 | 0.0000014 | 0.0002620 | regulation of nitric oxide biosynthetic process |
| GO:0044712 | 499 | 18 | 0.0000016 | 0.0002869 | single-organism catabolic process |
| GO:0010033 | 1304 | 31 | 0.0000025 | 0.0004221 | response to organic substance |
| GO:0007049 | 861 | 24 | 0.0000028 | 0.0004418 | cell cycle |
| GO:0006793 | 1183 | 29 | 0.0000030 | 0.0004471 | phosphorus metabolic process |
| GO:0090066 | 196 | 11 | 0.0000031 | 0.0004471 | regulation of anatomical structure size |
| GO:0022402 | 691 | 21 | 0.0000032 | 0.0004471 | cell cycle process |
| GO:0006796 | 1158 | 28 | 0.0000059 | 0.0007767 | phosphate-containing compound metabolic process |
| GO:0045597 | 443 | 16 | 0.0000061 | 0.0007767 | positive regulation of cell differentiation |
| GO:0009966 | 1299 | 30 | 0.0000066 | 0.0008001 | regulation of signal transduction |
| GO:0000278 | 558 | 18 | 0.0000076 | 0.0008852 | mitotic cell cycle |
| GO:0009719 | 734 | 21 | 0.0000082 | 0.0009205 | response to endogenous stimulus |
| GO:0010605 | 1250 | 29 | 0.0000088 | 0.0009439 | negative regulation of macromolecule metabolic process |
| GO:1903426 | 30 | 5 | 0.0000090 | 0.0009439 | regulation of reactive oxygen species biosynthetic process |
| GO:0050767 | 358 | 14 | 0.0000098 | 0.0009913 | regulation of neurogenesis |
| GO:0051960 | 410 | 15 | 0.0000104 | 0.0009987 | regulation of nervous system development |
| GO:0033036 | 1262 | 29 | 0.0000105 | 0.0009987 | macromolecule localization |
| GO:0071702 | 1130 | 27 | 0.0000110 | 0.0010116 | organic substance transport |
| GO:0006260 | 147 | 9 | 0.0000125 | 0.0010854 | DNA replication |
| GO:0051240 | 695 | 20 | 0.0000125 | 0.0010854 | positive regulation of multicellular organismal process |
| GO:0050790 | 1280 | 29 | 0.0000137 | 0.0011585 | regulation of catalytic activity |
| GO:0042592 | 642 | 19 | 0.0000141 | 0.0011615 | homeostatic process |
| GO:0048699 | 766 | 21 | 0.0000155 | 0.0012418 | generation of neurons |
| GO:0048011 | 195 | 10 | 0.0000194 | 0.0015109 | neurotrophin TRK receptor signaling pathway |
| GO:0038179 | 198 | 10 | 0.0000221 | 0.0016802 | neurotrophin signaling pathway |
| GO:0051051 | 243 | 11 | 0.0000238 | 0.0017255 | negative regulation of transport |
| GO:0009892 | 1389 | 30 | 0.0000238 | 0.0017255 | negative regulation of metabolic process |
| GO:0060284 | 444 | 15 | 0.0000263 | 0.0018199 | regulation of cell development |
| GO:0048598 | 293 | 12 | 0.0000273 | 0.0018199 | embryonic morphogenesis |
| GO:0006261 | 62 | 6 | 0.0000282 | 0.0018199 | DNA-dependent DNA replication |
| GO:0033260 | 19 | 4 | 0.0000283 | 0.0018199 | nuclear DNA replication |
| GO:0044786 | 19 | 4 | 0.0000283 | 0.0018199 | cell cycle DNA replication |
| GO:0045892 | 617 | 18 | 0.0000290 | 0.0018199 | negative regulation of transcription, DNA-templated |
| GO:0051130 | 677 | 19 | 0.0000293 | 0.0018199 | positive regulation of cellular component organization |
| GO:0045664 | 297 | 12 | 0.0000311 | 0.0018663 | regulation of neuron differentiation |
| GO:0010604 | 1481 | 31 | 0.0000313 | 0.0018663 | positive regulation of macromolecule metabolic process |
| GO:0010821 | 207 | 10 | 0.0000323 | 0.0018909 | regulation of mitochondrion organization |
| GO:0051704 | 1069 | 25 | 0.0000341 | 0.0019599 | multi-organism process |
| GO:0010629 | 810 | 21 | 0.0000352 | 0.0019850 | negative regulation of gene expression |
| GO:0048513 | 1351 | 29 | 0.0000370 | 0.0020485 | organ development |
| GO:0043279 | 66 | 6 | 0.0000404 | 0.0021573 | response to alkaloid |
| GO:0080135 | 461 | 15 | 0.0000404 | 0.0021573 | regulation of cellular response to stress |
| GO:0016310 | 697 | 19 | 0.0000434 | 0.0022783 | phosphorylation |
| GO:0051246 | 1373 | 29 | 0.0000495 | 0.0025538 | regulation of protein metabolic process |
| GO:2000113 | 709 | 19 | 0.0000546 | 0.0027669 | negative regulation of cellular macromolecule biosynthetic process |
| GO:0060249 | 138 | 8 | 0.0000564 | 0.0028141 | anatomical structure homeostasis |
| GO:0010822 | 182 | 9 | 0.0000673 | 0.0032997 | positive regulation of mitochondrion organization |
| GO:0033043 | 660 | 18 | 0.0000691 | 0.0033144 | regulation of organelle organization |
| GO:0051000 | 9 | 3 | 0.0000697 | 0.0033144 | positive regulation of nitric-oxide synthase activity |
| GO:0071363 | 376 | 13 | 0.0000725 | 0.0033746 | cellular response to growth factor stimulus |
| GO:0060341 | 663 | 18 | 0.0000732 | 0.0033746 | regulation of cellular localization |
| GO:0080134 | 798 | 20 | 0.0000868 | 0.0039075 | regulation of response to stress |
| GO:0007166 | 1134 | 25 | 0.0000883 | 0.0039075 | cell surface receptor signaling pathway |
| GO:1902589 | 1276 | 27 | 0.0000899 | 0.0039075 | single-organism organelle organization |
| GO:0022603 | 495 | 15 | 0.0000899 | 0.0039075 | regulation of anatomical structure morphogenesis |
| GO:0070848 | 386 | 13 | 0.0000944 | 0.0040452 | response to growth factor |
| GO:0038095 | 111 | 7 | 0.0000976 | 0.0041218 | Fc-epsilon receptor signaling pathway |
| GO:0032770 | 10 | 3 | 0.0000989 | 0.0041218 | positive regulation of monooxygenase activity |
| GO:0022008 | 807 | 20 | 0.0001010 | 0.0041249 | neurogenesis |
| GO:0048646 | 559 | 16 | 0.0001017 | 0.0041249 | anatomical structure formation involved in morphogenesis |
| GO:0006312 | 26 | 4 | 0.0001036 | 0.0041456 | mitotic recombination |
| GO:0009628 | 622 | 17 | 0.0001077 | 0.0042542 | response to abiotic stimulus |
| GO:0032268 | 1291 | 27 | 0.0001091 | 0.0042542 | regulation of cellular protein metabolic process |
| GO:0070887 | 1221 | 26 | 0.0001109 | 0.0042705 | cellular response to chemical stimulus |
| GO:1903507 | 625 | 17 | 0.0001141 | 0.0043405 | negative regulation of nucleic acid-templated transcription |
| GO:0050900 | 115 | 7 | 0.0001219 | 0.0045690 | leukocyte migration |
| GO:0031324 | 1229 | 26 | 0.0001232 | 0.0045690 | negative regulation of cellular metabolic process |
| GO:1902679 | 631 | 17 | 0.0001280 | 0.0046601 | negative regulation of RNA biosynthetic process |
| GO:0007059 | 116 | 7 | 0.0001287 | 0.0046601 | chromosome segregation |
| GO:0009056 | 1026 | 23 | 0.0001351 | 0.0047785 | catabolic process |
| GO:0032446 | 456 | 14 | 0.0001351 | 0.0047785 | protein modification by small protein conjugation |
| GO:0051641 | 1312 | 27 | 0.0001422 | 0.0049716 | cellular localization |
| GO:0014070 | 403 | 13 | 0.0001448 | 0.0050023 | response to organic cyclic compound |
| GO:0031327 | 765 | 19 | 0.0001474 | 0.0050023 | negative regulation of cellular biosynthetic process |
| GO:0006468 | 519 | 15 | 0.0001512 | 0.0050023 | protein phosphorylation |
| GO:0009894 | 519 | 15 | 0.0001512 | 0.0050023 | regulation of catabolic process |
| GO:1901698 | 461 | 14 | 0.0001513 | 0.0050023 | response to nitrogen compound |
| GO:1901575 | 901 | 21 | 0.0001582 | 0.0051597 | organic substance catabolic process |
| GO:1902531 | 770 | 19 | 0.0001603 | 0.0051597 | regulation of intracellular signal transduction |
| GO:0008283 | 353 | 12 | 0.0001611 | 0.0051597 | cell proliferation |
| GO:0009605 | 903 | 21 | 0.0001630 | 0.0051665 | response to external stimulus |
| GO:1903828 | 85 | 6 | 0.0001672 | 0.0052430 | negative regulation of cellular protein localization |
| GO:0009890 | 777 | 19 | 0.0001799 | 0.0055835 | negative regulation of biosynthetic process |
| GO:0006357 | 913 | 21 | 0.0001895 | 0.0058218 | regulation of transcription from RNA polymerase II promoter |
| GO:0051172 | 783 | 19 | 0.0001983 | 0.0060332 | negative regulation of nitrogen compound metabolic process |
| GO:0048871 | 125 | 7 | 0.0002047 | 0.0060944 | multicellular organismal homeostasis |
| GO:0070647 | 534 | 15 | 0.0002058 | 0.0060944 | protein modification by small protein conjugation or removal |
| GO:0023057 | 657 | 17 | 0.0002064 | 0.0060944 | negative regulation of signaling |
| GO:0060429 | 477 | 14 | 0.0002149 | 0.0062863 | epithelium development |
| GO:0051253 | 661 | 17 | 0.0002215 | 0.0064183 | negative regulation of RNA metabolic process |
| GO:0010243 | 422 | 13 | 0.0002270 | 0.0064702 | response to organonitrogen compound |
| GO:0071310 | 994 | 22 | 0.0002276 | 0.0064702 | cellular response to organic substance |
| GO:0048534 | 314 | 11 | 0.0002336 | 0.0065526 | hematopoietic or lymphoid organ development |
| GO:0043085 | 860 | 20 | 0.0002348 | 0.0065526 | positive regulation of catalytic activity |
| GO:0010648 | 665 | 17 | 0.0002377 | 0.0065733 | negative regulation of cell communication |
| GO:0051248 | 604 | 16 | 0.0002450 | 0.0066722 | negative regulation of protein metabolic process |
| GO:0048585 | 731 | 18 | 0.0002457 | 0.0066722 | negative regulation of response to stimulus |
| GO:0008104 | 1071 | 23 | 0.0002515 | 0.0067700 | protein localization |
| GO:0051093 | 428 | 13 | 0.0002602 | 0.0069426 | negative regulation of developmental process |
| GO:0021520 | 3 | 2 | 0.0002723 | 0.0070789 | spinal cord motor neuron cell fate specification |
| GO:0021521 | 3 | 2 | 0.0002723 | 0.0070789 | ventral spinal cord interneuron specification |
| GO:0060573 | 3 | 2 | 0.0002723 | 0.0070789 | cell fate specification involved in pattern specification |
| GO:0010558 | 738 | 18 | 0.0002756 | 0.0071048 | negative regulation of macromolecule biosynthetic process |
| GO:0007009 | 133 | 7 | 0.0002995 | 0.0076568 | plasma membrane organization |
| GO:0034220 | 435 | 13 | 0.0003040 | 0.0077067 | ion transmembrane transport |
| GO:0044281 | 1234 | 25 | 0.0003238 | 0.0081397 | small molecule metabolic process |
| GO:0001933 | 225 | 9 | 0.0003318 | 0.0082649 | negative regulation of protein phosphorylation |
| GO:0031331 | 275 | 10 | 0.0003342 | 0.0082649 | positive regulation of cellular catabolic process |
| GO:0051353 | 15 | 3 | 0.0003620 | 0.0088809 | positive regulation of oxidoreductase activity |
| GO:0002520 | 331 | 11 | 0.0003658 | 0.0089029 | immune system development |
| GO:1903047 | 505 | 14 | 0.0003824 | 0.0092316 | mitotic cell cycle process |
| GO:0010975 | 231 | 9 | 0.0004020 | 0.0095691 | regulation of neuron projection development |
| GO:0006310 | 140 | 7 | 0.0004088 | 0.0095691 | DNA recombination |
| GO:0007173 | 140 | 7 | 0.0004088 | 0.0095691 | epidermal growth factor receptor signaling pathway |
| GO:0045785 | 184 | 8 | 0.0004089 | 0.0095691 | positive regulation of cell adhesion |
| GO:0016032 | 450 | 13 | 0.0004196 | 0.0097431 | viral process |
| GO:0044764 | 452 | 13 | 0.0004375 | 0.0097455 | multi-organism cellular process |
| GO:0072358 | 452 | 13 | 0.0004375 | 0.0097455 | cardiovascular system development |
| GO:0072359 | 452 | 13 | 0.0004375 | 0.0097455 | circulatory system development |
| GO:0009790 | 512 | 14 | 0.0004385 | 0.0097455 | embryo development |
| GO:0045429 | 16 | 3 | 0.0004424 | 0.0097455 | positive regulation of nitric oxide biosynthetic process |
| GO:1904407 | 16 | 3 | 0.0004424 | 0.0097455 | positive regulation of nitric oxide metabolic process |
| GO:0042325 | 702 | 17 | 0.0004428 | 0.0097455 | regulation of phosphorylation |
| GO:0038127 | 142 | 7 | 0.0004453 | 0.0097455 | ERBB signaling pathway |
| GO:0042063 | 102 | 6 | 0.0004501 | 0.0097790 | gliogenesis |
| GO:0006259 | 455 | 13 | 0.0004656 | 0.0100146 | DNA metabolic process |
| GO:2000379 | 38 | 4 | 0.0004675 | 0.0100146 | positive regulation of reactive oxygen species metabolic process |
| GO:0021915 | 103 | 6 | 0.0004741 | 0.0100861 | neural tube development |
| GO:0048878 | 398 | 12 | 0.0004785 | 0.0101082 | chemical homeostasis |
| GO:0055085 | 579 | 15 | 0.0004832 | 0.0101378 | transmembrane transport |
| GO:0010506 | 190 | 8 | 0.0005060 | 0.0104178 | regulation of autophagy |
| GO:0003333 | 39 | 4 | 0.0005170 | 0.0104178 | amino acid transmembrane transport |
| GO:0009888 | 779 | 18 | 0.0005234 | 0.0104178 | tissue development |
| GO:0006289 | 69 | 5 | 0.0005246 | 0.0104178 | nucleotide-excision repair |
| GO:0019953 | 346 | 11 | 0.0005302 | 0.0104178 | sexual reproduction |
| GO:0006297 | 17 | 3 | 0.0005334 | 0.0104178 | nucleotide-excision repair, DNA gap filling |
| GO:0055081 | 17 | 3 | 0.0005334 | 0.0104178 | anion homeostasis |
| GO:0007276 | 292 | 10 | 0.0005347 | 0.0104178 | gamete generation |
| GO:0001710 | 4 | 2 | 0.0005411 | 0.0104178 | mesodermal cell fate commitment |
| GO:0021514 | 4 | 2 | 0.0005411 | 0.0104178 | ventral spinal cord interneuron differentiation |
| GO:0045792 | 4 | 2 | 0.0005411 | 0.0104178 | negative regulation of cell size |
| GO:0060579 | 4 | 2 | 0.0005411 | 0.0104178 | ventral spinal cord interneuron fate commitment |
| GO:0060581 | 4 | 2 | 0.0005411 | 0.0104178 | cell fate commitment involved in pattern specification |
| GO:0038093 | 147 | 7 | 0.0005479 | 0.0104831 | Fc receptor signaling pathway |
| GO:0010647 | 851 | 19 | 0.0005561 | 0.0105727 | positive regulation of cell communication |
| GO:0007389 | 193 | 8 | 0.0005612 | 0.0105851 | pattern specification process |
| GO:0030097 | 294 | 10 | 0.0005637 | 0.0105851 | hemopoiesis |
| GO:0006811 | 589 | 15 | 0.0005766 | 0.0107504 | ion transport |
| GO:0042326 | 243 | 9 | 0.0005796 | 0.0107504 | negative regulation of phosphorylation |
| GO:0045934 | 720 | 17 | 0.0005887 | 0.0107628 | negative regulation of nucleobase-containing compound metabolic process |
| GO:0001932 | 655 | 16 | 0.0005946 | 0.0107628 | regulation of protein phosphorylation |
| GO:0008285 | 351 | 11 | 0.0005971 | 0.0107628 | negative regulation of cell proliferation |
| GO:0032386 | 351 | 11 | 0.0005971 | 0.0107628 | regulation of intracellular transport |
| GO:0042127 | 721 | 17 | 0.0005979 | 0.0107628 | regulation of cell proliferation |
| GO:0048285 | 297 | 10 | 0.0006097 | 0.0109105 | organelle fission |
| GO:0006284 | 41 | 4 | 0.0006272 | 0.0110919 | base-excision repair |
| GO:0019985 | 41 | 4 | 0.0006272 | 0.0110919 | translesion synthesis |
| GO:0032201 | 18 | 3 | 0.0006356 | 0.0111766 | telomere maintenance via semi-conservative replication |
| GO:0036293 | 151 | 7 | 0.0006429 | 0.0112395 | response to decreased oxygen levels |
| GO:2000377 | 73 | 5 | 0.0006798 | 0.0117804 | regulation of reactive oxygen species metabolic process |
| GO:0044093 | 1006 | 21 | 0.0006816 | 0.0117804 | positive regulation of molecular function |
| GO:0031344 | 302 | 10 | 0.0006933 | 0.0119156 | regulation of cell projection organization |
| GO:0007167 | 538 | 14 | 0.0007128 | 0.0121716 | enzyme linked receptor protein signaling pathway |
| GO:0010628 | 939 | 20 | 0.0007162 | 0.0121716 | positive regulation of gene expression |
| GO:0008643 | 74 | 5 | 0.0007235 | 0.0121963 | carbohydrate transport |
| GO:1901564 | 940 | 20 | 0.0007257 | 0.0121963 | organonitrogen compound metabolic process |
| GO:0008543 | 112 | 6 | 0.0007390 | 0.0123518 | fibroblast growth factor receptor signaling pathway |
| GO:0009896 | 306 | 10 | 0.0007668 | 0.0126532 | positive regulation of catabolic process |
| GO:0048010 | 75 | 5 | 0.0007692 | 0.0126532 | vascular endothelial growth factor receptor signaling pathway |
| GO:0033993 | 362 | 11 | 0.0007695 | 0.0126532 | response to lipid |
| GO:0044403 | 481 | 13 | 0.0007800 | 0.0126880 | symbiosis, encompassing mutualism through parasitism |
| GO:0044419 | 481 | 13 | 0.0007800 | 0.0126880 | interspecies interaction between organisms |
| GO:0051241 | 483 | 13 | 0.0008102 | 0.0131097 | negative regulation of multicellular organismal process |
| GO:0000122 | 424 | 12 | 0.0008331 | 0.0134090 | negative regulation of transcription from RNA polymerase II promoter |
| GO:1903146 | 115 | 6 | 0.0008488 | 0.0135905 | regulation of mitophagy |
| GO:0006790 | 206 | 8 | 0.0008590 | 0.0136791 | sulfur compound metabolic process |
| GO:0030182 | 549 | 14 | 0.0008665 | 0.0136791 | neuron differentiation |
| GO:0019220 | 814 | 18 | 0.0008689 | 0.0136791 | regulation of phosphate metabolic process |
| GO:0010563 | 312 | 10 | 0.0008890 | 0.0136791 | negative regulation of phosphorus metabolic process |
| GO:0045936 | 312 | 10 | 0.0008890 | 0.0136791 | negative regulation of phosphate metabolic process |
| GO:0007422 | 45 | 4 | 0.0008956 | 0.0136791 | peripheral nervous system development |
| GO:0048665 | 5 | 2 | 0.0008961 | 0.0136791 | neuron fate specification |
| GO:0071636 | 5 | 2 | 0.0008961 | 0.0136791 | positive regulation of transforming growth factor beta production |
| GO:1990822 | 5 | 2 | 0.0008961 | 0.0136791 | basic amino acid transmembrane transport |
| GO:0010638 | 369 | 11 | 0.0008993 | 0.0136791 | positive regulation of organelle organization |
| GO:0010001 | 78 | 5 | 0.0009194 | 0.0139139 | glial cell differentiation |
| GO:0022604 | 314 | 10 | 0.0009331 | 0.0140343 | regulation of cell morphogenesis |
| GO:0051962 | 260 | 9 | 0.0009365 | 0.0140343 | positive regulation of nervous system development |
| GO:0007169 | 431 | 12 | 0.0009594 | 0.0143064 | transmembrane receptor protein tyrosine kinase signaling pathway |
| GO:1903827 | 316 | 10 | 0.0009790 | 0.0145277 | regulation of cellular protein localization |
| GO:0051174 | 824 | 18 | 0.0009979 | 0.0147360 | regulation of phosphorus metabolic process |
| GO:1903428 | 21 | 3 | 0.0010143 | 0.0149060 | positive regulation of reactive oxygen species biosynthetic process |
| GO:0051301 | 318 | 10 | 0.0010268 | 0.0150050 | cell division |
| GO:0001894 | 80 | 5 | 0.0010309 | 0.0150050 | tissue homeostasis |
| GO:0045596 | 319 | 10 | 0.0010513 | 0.0151255 | negative regulation of cell differentiation |
| GO:0006301 | 47 | 4 | 0.0010563 | 0.0151255 | postreplication repair |
| GO:0072527 | 47 | 4 | 0.0010563 | 0.0151255 | pyrimidine-containing compound metabolic process |
| GO:0009725 | 436 | 12 | 0.0010591 | 0.0151255 | response to hormone |
| GO:0008064 | 81 | 5 | 0.0010903 | 0.0154267 | regulation of actin polymerization or depolymerization |
| GO:0046434 | 81 | 5 | 0.0010903 | 0.0154267 | organophosphate catabolic process |
| GO:0006366 | 438 | 12 | 0.0011013 | 0.0155099 | transcription from RNA polymerase II promoter |
| GO:0070482 | 166 | 7 | 0.0011210 | 0.0156976 | response to oxygen levels |
| GO:0001838 | 82 | 5 | 0.0011522 | 0.0156976 | embryonic epithelial tube formation |
| GO:0030832 | 82 | 5 | 0.0011522 | 0.0156976 | regulation of actin filament length |
| GO:0072175 | 82 | 5 | 0.0011522 | 0.0156976 | epithelial tube formation |
| GO:0044344 | 122 | 6 | 0.0011541 | 0.0156976 | cellular response to fibroblast growth factor stimulus |
| GO:0043010 | 167 | 7 | 0.0011607 | 0.0156976 | camera-type eye development |
| GO:0000722 | 22 | 3 | 0.0011662 | 0.0156976 | telomere maintenance via recombination |
| GO:0006298 | 22 | 3 | 0.0011662 | 0.0156976 | mismatch repair |
| GO:0042220 | 22 | 3 | 0.0011662 | 0.0156976 | response to cocaine |
| GO:0043491 | 22 | 3 | 0.0011662 | 0.0156976 | protein kinase B signaling |
| GO:0071774 | 123 | 6 | 0.0012038 | 0.0161240 | response to fibroblast growth factor |
| GO:0031399 | 909 | 19 | 0.0012135 | 0.0161240 | regulation of protein modification process |
| GO:1901137 | 383 | 11 | 0.0012138 | 0.0161240 | carbohydrate derivative biosynthetic process |
| GO:0031400 | 384 | 11 | 0.0012394 | 0.0163918 | negative regulation of protein modification process |
| GO:1903649 | 271 | 9 | 0.0012505 | 0.0164676 | regulation of cytoplasmic transport |
| GO:0045184 | 842 | 18 | 0.0012717 | 0.0166749 | establishment of protein localization |
| GO:0008361 | 84 | 5 | 0.0012838 | 0.0167606 | regulation of cell size |
| GO:0051224 | 125 | 6 | 0.0013080 | 0.0170042 | negative regulation of protein transport |
| GO:0014037 | 23 | 3 | 0.0013317 | 0.0170724 | Schwann cell differentiation |
| GO:0055089 | 6 | 2 | 0.0013357 | 0.0170724 | fatty acid homeostasis |
| GO:0097011 | 6 | 2 | 0.0013357 | 0.0170724 | cellular response to granulocyte macrophage colony-stimulating factor stimulus |
| GO:0097012 | 6 | 2 | 0.0013357 | 0.0170724 | response to granulocyte macrophage colony-stimulating factor |
| GO:0012501 | 641 | 15 | 0.0013495 | 0.0171563 | programmed cell death |
| GO:0050870 | 85 | 5 | 0.0013536 | 0.0171563 | positive regulation of T cell activation |
| GO:0000003 | 449 | 12 | 0.0013593 | 0.0171573 | reproduction |
| GO:0031329 | 451 | 12 | 0.0014112 | 0.0177387 | regulation of cellular catabolic process |
| GO:0015758 | 51 | 4 | 0.0014365 | 0.0179094 | glucose transport |
| GO:0060359 | 51 | 4 | 0.0014365 | 0.0179094 | response to ammonium ion |
| GO:0033365 | 334 | 10 | 0.0014816 | 0.0183961 | protein localization to organelle |
| GO:0034112 | 87 | 5 | 0.0015015 | 0.0185380 | positive regulation of homotypic cell-cell adhesion |
| GO:0046329 | 24 | 3 | 0.0015113 | 0.0185380 | negative regulation of JNK cascade |
| GO:0050999 | 24 | 3 | 0.0015113 | 0.0185380 | regulation of nitric-oxide synthase activity |
| GO:0071705 | 279 | 9 | 0.0015283 | 0.0185731 | nitrogen compound transport |
| GO:0001704 | 52 | 4 | 0.0015447 | 0.0185731 | formation of primary germ layer |
| GO:0006694 | 52 | 4 | 0.0015447 | 0.0185731 | steroid biosynthetic process |
| GO:0008645 | 52 | 4 | 0.0015447 | 0.0185731 | hexose transport |
| GO:0015749 | 52 | 4 | 0.0015447 | 0.0185731 | monosaccharide transport |
| GO:1903039 | 88 | 5 | 0.0015797 | 0.0189195 | positive regulation of leukocyte cell-cell adhesion |
| GO:0042981 | 722 | 16 | 0.0016430 | 0.0194332 | regulation of apoptotic process |
| GO:0048584 | 1006 | 20 | 0.0016444 | 0.0194332 | positive regulation of response to stimulus |
| GO:0010942 | 339 | 10 | 0.0016534 | 0.0194332 | positive regulation of cell death |
| GO:0030278 | 89 | 5 | 0.0016610 | 0.0194332 | regulation of ossification |
| GO:0098779 | 89 | 5 | 0.0016610 | 0.0194332 | mitophagy in response to mitochondrial depolarization |
| GO:0098780 | 89 | 5 | 0.0016610 | 0.0194332 | response to mitochondrial depolarisation |
| GO:0006271 | 25 | 3 | 0.0017054 | 0.0197252 | DNA strand elongation involved in DNA replication |
| GO:0022616 | 25 | 3 | 0.0017054 | 0.0197252 | DNA strand elongation |
| GO:0034405 | 25 | 3 | 0.0017054 | 0.0197252 | response to fluid shear stress |
| GO:0015031 | 795 | 17 | 0.0017267 | 0.0198962 | protein transport |
| GO:0043067 | 727 | 16 | 0.0017619 | 0.0202026 | regulation of programmed cell death |
| GO:0010634 | 54 | 4 | 0.0017778 | 0.0202026 | positive regulation of epithelial cell migration |
| GO:0007264 | 402 | 11 | 0.0017805 | 0.0202026 | small GTPase mediated signal transduction |
| GO:0010959 | 180 | 7 | 0.0017849 | 0.0202026 | regulation of metal ion transport |
| GO:0034613 | 728 | 16 | 0.0017865 | 0.0202026 | cellular protein localization |
| GO:0035148 | 91 | 5 | 0.0018325 | 0.0204807 | tube formation |
| GO:1903599 | 91 | 5 | 0.0018325 | 0.0204807 | positive regulation of mitophagy |
| GO:0015802 | 7 | 2 | 0.0018582 | 0.0204807 | basic amino acid transport |
| GO:0065005 | 7 | 2 | 0.0018582 | 0.0204807 | protein-lipid complex assembly |
| GO:0070862 | 7 | 2 | 0.0018582 | 0.0204807 | negative regulation of protein exit from endoplasmic reticulum |
| GO:0097062 | 7 | 2 | 0.0018582 | 0.0204807 | dendritic spine maintenance |
| GO:1904153 | 7 | 2 | 0.0018582 | 0.0204807 | negative regulation of retrograde protein transport, ER to cytosol |
| GO:0006469 | 134 | 6 | 0.0018650 | 0.0204817 | negative regulation of protein kinase activity |
| GO:1900034 | 55 | 4 | 0.0019031 | 0.0208181 | regulation of cellular response to heat |
| GO:0042769 | 26 | 3 | 0.0019143 | 0.0208181 | DNA damage response, detection of DNA damage |
| GO:0010632 | 92 | 5 | 0.0019230 | 0.0208181 | regulation of epithelial cell migration |
| GO:0016331 | 92 | 5 | 0.0019230 | 0.0208181 | morphogenesis of embryonic epithelium |
| GO:0070727 | 734 | 16 | 0.0019404 | 0.0209318 | cellular macromolecule localization |
| GO:0044248 | 877 | 18 | 0.0019901 | 0.0213694 | cellular catabolic process |
| GO:1901135 | 600 | 14 | 0.0019950 | 0.0213694 | carbohydrate derivative metabolic process |
| GO:0030203 | 94 | 5 | 0.0021138 | 0.0225618 | glycosaminoglycan metabolic process |
| GO:0051649 | 1103 | 21 | 0.0021298 | 0.0225879 | establishment of localization in cell |
| GO:0008219 | 672 | 15 | 0.0021333 | 0.0225879 | cell death |
| GO:0032768 | 27 | 3 | 0.0021385 | 0.0225879 | regulation of monooxygenase activity |
| GO:0051173 | 957 | 19 | 0.0021797 | 0.0229434 | positive regulation of nitrogen compound metabolic process |
| GO:0016265 | 674 | 15 | 0.0021947 | 0.0230219 | death |
| GO:0010769 | 187 | 7 | 0.0022148 | 0.0231522 | regulation of cell morphogenesis involved in differentiation |
| GO:0016241 | 139 | 6 | 0.0022434 | 0.0233385 | regulation of macroautophagy |
| GO:0071495 | 542 | 13 | 0.0022624 | 0.0233385 | cellular response to endogenous stimulus |
| GO:0044703 | 415 | 11 | 0.0022805 | 0.0233385 | multi-organism reproductive process |
| GO:0001654 | 188 | 7 | 0.0022822 | 0.0233385 | eye development |
| GO:0044723 | 355 | 10 | 0.0023144 | 0.0233385 | single-organism carbohydrate metabolic process |
| GO:0006023 | 58 | 4 | 0.0023153 | 0.0233385 | aminoglycan biosynthetic process |
| GO:0006024 | 58 | 4 | 0.0023153 | 0.0233385 | glycosaminoglycan biosynthetic process |
| GO:0009968 | 610 | 14 | 0.0023199 | 0.0233385 | negative regulation of signal transduction |
| GO:0003002 | 140 | 6 | 0.0023256 | 0.0233385 | regionalization |
| GO:0032103 | 189 | 7 | 0.0023511 | 0.0233385 | positive regulation of response to external stimulus |
| GO:0051129 | 356 | 10 | 0.0023619 | 0.0233385 | negative regulation of cellular component organization |
| GO:0051336 | 749 | 16 | 0.0023746 | 0.0233385 | regulation of hydrolase activity |
| GO:0009262 | 28 | 3 | 0.0023784 | 0.0233385 | deoxyribonucleotide metabolic process |
| GO:0010833 | 28 | 3 | 0.0023784 | 0.0233385 | telomere maintenance via telomere lengthening |
| GO:0030279 | 28 | 3 | 0.0023784 | 0.0233385 | negative regulation of ossification |
| GO:0032873 | 28 | 3 | 0.0023784 | 0.0233385 | negative regulation of stress-activated MAPK cascade |
| GO:0043535 | 28 | 3 | 0.0023784 | 0.0233385 | regulation of blood vessel endothelial cell migration |
| GO:0070303 | 28 | 3 | 0.0023784 | 0.0233385 | negative regulation of stress-activated protein kinase signaling cascade |
| GO:1902475 | 28 | 3 | 0.0023784 | 0.0233385 | L-alpha-amino acid transmembrane transport |
| GO:0040011 | 612 | 14 | 0.0023899 | 0.0233763 | locomotion |
| GO:0048609 | 358 | 10 | 0.0024593 | 0.0234778 | multicellular organismal reproductive process |
| GO:0009263 | 8 | 2 | 0.0024620 | 0.0234778 | deoxyribonucleotide biosynthetic process |
| GO:0014067 | 8 | 2 | 0.0024620 | 0.0234778 | negative regulation of phosphatidylinositol 3-kinase signaling |
| GO:0016559 | 8 | 2 | 0.0024620 | 0.0234778 | peroxisome fission |
| GO:0032733 | 8 | 2 | 0.0024620 | 0.0234778 | positive regulation of interleukin-10 production |
| GO:0060795 | 8 | 2 | 0.0024620 | 0.0234778 | cell fate commitment involved in formation of primary germ layer |
| GO:1904152 | 8 | 2 | 0.0024620 | 0.0234778 | regulation of retrograde protein transport, ER to cytosol |
| GO:1904293 | 8 | 2 | 0.0024620 | 0.0234778 | negative regulation of ERAD pathway |
| GO:0060627 | 244 | 8 | 0.0025030 | 0.0237942 | regulation of vesicle-mediated transport |
| GO:0006022 | 98 | 5 | 0.0025361 | 0.0239594 | aminoglycan metabolic process |
| GO:0043409 | 98 | 5 | 0.0025361 | 0.0239594 | negative regulation of MAPK cascade |
| GO:0006955 | 618 | 14 | 0.0026103 | 0.0245839 | immune response |
| GO:0033673 | 144 | 6 | 0.0026770 | 0.0250566 | negative regulation of kinase activity |
| GO:1901214 | 144 | 6 | 0.0026770 | 0.0250566 | regulation of neuron death |
| GO:0002682 | 689 | 15 | 0.0027043 | 0.0252342 | regulation of immune system process |
| GO:0030155 | 304 | 9 | 0.0027297 | 0.0253933 | regulation of cell adhesion |
| GO:0022409 | 100 | 5 | 0.0027688 | 0.0256013 | positive regulation of cell-cell adhesion |
| GO:0045765 | 100 | 5 | 0.0027688 | 0.0256013 | regulation of angiogenesis |
| GO:0090317 | 61 | 4 | 0.0027851 | 0.0256740 | negative regulation of intracellular protein transport |
| GO:0032504 | 366 | 10 | 0.0028814 | 0.0264814 | multicellular organism reproduction |
| GO:0000725 | 62 | 4 | 0.0029552 | 0.0270778 | recombinational repair |
| GO:0045087 | 494 | 12 | 0.0029896 | 0.0273101 | innate immune response |
| GO:0043087 | 370 | 10 | 0.0031132 | 0.0283171 | regulation of GTPase activity |
| GO:0051044 | 9 | 2 | 0.0031455 | 0.0283171 | positive regulation of membrane protein ectodomain proteolysis |
| GO:0071243 | 9 | 2 | 0.0031455 | 0.0283171 | cellular response to arsenic-containing substance |
| GO:0006915 | 631 | 14 | 0.0031458 | 0.0283171 | apoptotic process |
| GO:0016239 | 103 | 5 | 0.0031463 | 0.0283171 | positive regulation of macroautophagy |
| GO:0001666 | 149 | 6 | 0.0031706 | 0.0283973 | response to hypoxia |
| GO:0098655 | 311 | 9 | 0.0031739 | 0.0283973 | cation transmembrane transport |
| GO:0044702 | 498 | 12 | 0.0031899 | 0.0284217 | single organism reproductive process |
| GO:0001707 | 31 | 3 | 0.0031953 | 0.0284217 | mesoderm formation |
| GO:0010941 | 773 | 16 | 0.0032364 | 0.0287026 | regulation of cell death |
| GO:0006979 | 201 | 7 | 0.0033106 | 0.0290739 | response to oxidative stress |
| GO:0001843 | 64 | 4 | 0.0033165 | 0.0290739 | neural tube closure |
| GO:0010594 | 64 | 4 | 0.0033165 | 0.0290739 | regulation of endothelial cell migration |
| GO:0060606 | 64 | 4 | 0.0033165 | 0.0290739 | tube closure |
| GO:1902532 | 256 | 8 | 0.0033552 | 0.0293290 | negative regulation of intracellular signal transduction |
| GO:0032269 | 568 | 13 | 0.0033770 | 0.0293448 | negative regulation of cellular protein metabolic process |
| GO:0032104 | 151 | 6 | 0.0033859 | 0.0293448 | regulation of response to extracellular stimulus |
| GO:0032107 | 151 | 6 | 0.0033859 | 0.0293448 | regulation of response to nutrient levels |
| GO:0032106 | 105 | 5 | 0.0034178 | 0.0294529 | positive regulation of response to extracellular stimulus |
| GO:0032109 | 105 | 5 | 0.0034178 | 0.0294529 | positive regulation of response to nutrient levels |
| GO:0050776 | 439 | 11 | 0.0035010 | 0.0297170 | regulation of immune response |
| GO:0015807 | 32 | 3 | 0.0035012 | 0.0297170 | L-amino acid transport |
| GO:0031294 | 32 | 3 | 0.0035012 | 0.0297170 | lymphocyte costimulation |
| GO:0031295 | 32 | 3 | 0.0035012 | 0.0297170 | T cell costimulation |
| GO:0071897 | 65 | 4 | 0.0035079 | 0.0297170 | DNA biosynthetic process |
| GO:1903707 | 65 | 4 | 0.0035079 | 0.0297170 | negative regulation of hemopoiesis |
| GO:0007423 | 258 | 8 | 0.0035168 | 0.0297170 | sensory organ development |
| GO:0006508 | 640 | 14 | 0.0035670 | 0.0300575 | proteolysis |
| GO:0032956 | 153 | 6 | 0.0036120 | 0.0303528 | regulation of actin cytoskeleton organization |
| GO:0055114 | 574 | 13 | 0.0036892 | 0.0309159 | oxidation-reduction process |
| GO:0016925 | 66 | 4 | 0.0037066 | 0.0309768 | protein sumoylation |
| GO:0048332 | 33 | 3 | 0.0038245 | 0.0317414 | mesoderm morphogenesis |
| GO:0009612 | 108 | 5 | 0.0038559 | 0.0317414 | response to mechanical stimulus |
| GO:0043065 | 321 | 9 | 0.0039055 | 0.0317414 | positive regulation of apoptotic process |
| GO:0009223 | 10 | 2 | 0.0039072 | 0.0317414 | pyrimidine deoxyribonucleotide catabolic process |
| GO:0032653 | 10 | 2 | 0.0039072 | 0.0317414 | regulation of interleukin-10 production |
| GO:0048333 | 10 | 2 | 0.0039072 | 0.0317414 | mesodermal cell differentiation |
| GO:0048710 | 10 | 2 | 0.0039072 | 0.0317414 | regulation of astrocyte differentiation |
| GO:0070861 | 10 | 2 | 0.0039072 | 0.0317414 | regulation of protein exit from endoplasmic reticulum |
| GO:0014020 | 67 | 4 | 0.0039129 | 0.0317414 | primary neural tube formation |
| GO:0036294 | 67 | 4 | 0.0039129 | 0.0317414 | cellular response to decreased oxygen levels |
| GO:1903650 | 67 | 4 | 0.0039129 | 0.0317414 | negative regulation of cytoplasmic transport |
| GO:1901342 | 109 | 5 | 0.0040105 | 0.0324468 | regulation of vasculature development |
| GO:0030833 | 68 | 4 | 0.0041268 | 0.0332990 | regulation of actin filament polymerization |
| GO:0043068 | 324 | 9 | 0.0041489 | 0.0333889 | positive regulation of programmed cell death |
| GO:0071103 | 110 | 5 | 0.0041695 | 0.0334659 | DNA conformation change |
| GO:0044802 | 450 | 11 | 0.0042128 | 0.0337243 | single-organism membrane organization |
| GO:0032270 | 724 | 15 | 0.0042821 | 0.0341894 | positive regulation of cellular protein metabolic process |
| GO:0016567 | 388 | 10 | 0.0043470 | 0.0345800 | protein ubiquitination |
| GO:0043086 | 452 | 11 | 0.0043538 | 0.0345800 | negative regulation of catalytic activity |
| GO:0007010 | 519 | 12 | 0.0044282 | 0.0350793 | cytoskeleton organization |
| GO:0006367 | 160 | 6 | 0.0044922 | 0.0354943 | transcription initiation from RNA polymerase II promoter |
| GO:0071345 | 269 | 8 | 0.0045164 | 0.0355608 | cellular response to cytokine stimulus |
| GO:0002260 | 35 | 3 | 0.0045240 | 0.0355608 | lymphocyte homeostasis |
| GO:0051090 | 213 | 7 | 0.0045437 | 0.0356236 | regulation of sequence-specific DNA binding transcription factor activity |
| GO:0043549 | 457 | 11 | 0.0047228 | 0.0363616 | regulation of kinase activity |
| GO:0006244 | 11 | 2 | 0.0047454 | 0.0363616 | pyrimidine nucleotide catabolic process |
| GO:0009130 | 11 | 2 | 0.0047454 | 0.0363616 | pyrimidine nucleoside monophosphate biosynthetic process |
| GO:0021513 | 11 | 2 | 0.0047454 | 0.0363616 | spinal cord dorsal/ventral patterning |
| GO:0030261 | 11 | 2 | 0.0047454 | 0.0363616 | chromosome condensation |
| GO:0044030 | 11 | 2 | 0.0047454 | 0.0363616 | regulation of DNA methylation |
| GO:0045453 | 11 | 2 | 0.0047454 | 0.0363616 | bone resorption |
| GO:0048009 | 11 | 2 | 0.0047454 | 0.0363616 | insulin-like growth factor receptor signaling pathway |
| GO:0051043 | 11 | 2 | 0.0047454 | 0.0363616 | regulation of membrane protein ectodomain proteolysis |
| GO:0043547 | 331 | 9 | 0.0047631 | 0.0364057 | positive regulation of GTPase activity |
| GO:1903825 | 71 | 4 | 0.0048156 | 0.0367147 | organic acid transmembrane transport |
| GO:0002088 | 36 | 3 | 0.0049008 | 0.0370855 | lens development in camera-type eye |
| GO:0051341 | 36 | 3 | 0.0049008 | 0.0370855 | regulation of oxidoreductase activity |
| GO:0071260 | 36 | 3 | 0.0049008 | 0.0370855 | cellular response to mechanical stimulus |
| GO:0001101 | 163 | 6 | 0.0049142 | 0.0370946 | response to acid chemical |
| GO:0005975 | 460 | 11 | 0.0049559 | 0.0373162 | carbohydrate metabolic process |
| GO:0051924 | 115 | 5 | 0.0050324 | 0.0376742 | regulation of calcium ion transport |
| GO:0010720 | 274 | 8 | 0.0050372 | 0.0376742 | positive regulation of cell development |
| GO:0044092 | 596 | 13 | 0.0050406 | 0.0376742 | negative regulation of molecular function |
| GO:1903510 | 72 | 4 | 0.0050614 | 0.0377370 | mucopolysaccharide metabolic process |
| GO:0032880 | 529 | 12 | 0.0051401 | 0.0382302 | regulation of protein localization |
| GO:1901700 | 668 | 14 | 0.0051812 | 0.0384417 | response to oxygen-containing compound |
| GO:0051251 | 116 | 5 | 0.0052191 | 0.0386292 | positive regulation of lymphocyte activation |
| GO:0010595 | 37 | 3 | 0.0052961 | 0.0390090 | positive regulation of endothelial cell migration |
| GO:0014013 | 37 | 3 | 0.0052961 | 0.0390090 | regulation of gliogenesis |
| GO:0071453 | 73 | 4 | 0.0053154 | 0.0390565 | cellular response to oxygen levels |
| GO:0051249 | 166 | 6 | 0.0053647 | 0.0392727 | regulation of lymphocyte activation |
| GO:0051345 | 532 | 12 | 0.0053706 | 0.0392727 | positive regulation of hydrolase activity |
| GO:0034762 | 220 | 7 | 0.0054074 | 0.0393756 | regulation of transmembrane transport |
| GO:0010508 | 117 | 5 | 0.0054107 | 0.0393756 | positive regulation of autophagy |
| GO:0048468 | 890 | 17 | 0.0054235 | 0.0393756 | cell development |
| GO:0000280 | 278 | 8 | 0.0054861 | 0.0397347 | nuclear division |
| GO:0009129 | 12 | 2 | 0.0056587 | 0.0405271 | pyrimidine nucleoside monophosphate metabolic process |
| GO:0043536 | 12 | 2 | 0.0056587 | 0.0405271 | positive regulation of blood vessel endothelial cell migration |
| GO:0071498 | 12 | 2 | 0.0056587 | 0.0405271 | cellular response to fluid shear stress |
| GO:0071634 | 12 | 2 | 0.0056587 | 0.0405271 | regulation of transforming growth factor beta production |
| GO:0042493 | 222 | 7 | 0.0056754 | 0.0405271 | response to drug |
| GO:0044772 | 222 | 7 | 0.0056754 | 0.0405271 | mitotic cell cycle phase transition |
| GO:0001776 | 38 | 3 | 0.0057100 | 0.0405835 | leukocyte homeostasis |
| GO:0006220 | 38 | 3 | 0.0057100 | 0.0405835 | pyrimidine nucleotide metabolic process |
| GO:2001235 | 119 | 5 | 0.0058085 | 0.0411879 | positive regulation of apoptotic signaling pathway |
| GO:0022407 | 169 | 6 | 0.0058447 | 0.0412800 | regulation of cell-cell adhesion |
| GO:0001841 | 75 | 4 | 0.0058487 | 0.0412800 | neural tube formation |
| GO:0051050 | 471 | 11 | 0.0058897 | 0.0414730 | positive regulation of transport |
| GO:0051276 | 540 | 12 | 0.0060259 | 0.0423343 | chromosome organization |
| GO:0051254 | 826 | 16 | 0.0060748 | 0.0425799 | positive regulation of RNA metabolic process |
| GO:0044770 | 225 | 7 | 0.0060959 | 0.0426292 | cell cycle phase transition |
| GO:0071300 | 39 | 3 | 0.0061427 | 0.0428582 | cellular response to retinoic acid |
| GO:0050769 | 226 | 7 | 0.0062411 | 0.0434450 | positive regulation of neurogenesis |
| GO:0051338 | 543 | 12 | 0.0062874 | 0.0436672 | regulation of transferase activity |
| GO:0030100 | 122 | 5 | 0.0064434 | 0.0446488 | regulation of endocytosis |
| GO:0002683 | 173 | 6 | 0.0065326 | 0.0450617 | negative regulation of immune system process |
| GO:0071396 | 173 | 6 | 0.0065326 | 0.0450617 | cellular response to lipid |
| GO:0044085 | 1218 | 21 | 0.0066446 | 0.0453403 | cellular component biogenesis |
| GO:0009219 | 13 | 2 | 0.0066456 | 0.0453403 | pyrimidine deoxyribonucleotide metabolic process |
| GO:0015949 | 13 | 2 | 0.0066456 | 0.0453403 | nucleobase-containing small molecule interconversion |
| GO:0021511 | 13 | 2 | 0.0066456 | 0.0453403 | spinal cord patterning |
| GO:0048870 | 413 | 10 | 0.0066677 | 0.0453403 | cell motility |
| GO:0051674 | 413 | 10 | 0.0066677 | 0.0453403 | localization of cell |
| GO:0009653 | 1140 | 20 | 0.0066806 | 0.0453403 | anatomical structure morphogenesis |
| GO:0002768 | 229 | 7 | 0.0066922 | 0.0453403 | immune response-regulating cell surface receptor signaling pathway |
| GO:0032387 | 78 | 4 | 0.0067136 | 0.0453842 | negative regulation of intracellular transport |
| GO:0002764 | 288 | 8 | 0.0067418 | 0.0454449 | immune response-regulating signaling pathway |
| GO:0016482 | 480 | 11 | 0.0067525 | 0.0454449 | cytoplasmic transport |
| GO:0022414 | 549 | 12 | 0.0068373 | 0.0458838 | reproductive process |
| GO:0031667 | 230 | 7 | 0.0068479 | 0.0458838 | response to nutrient levels |
| GO:0050863 | 124 | 5 | 0.0068927 | 0.0460829 | regulation of T cell activation |
| GO:0048666 | 482 | 11 | 0.0069571 | 0.0464109 | neuron development |
| GO:0071496 | 176 | 6 | 0.0070858 | 0.0471664 | cellular response to external stimulus |
| GO:0043414 | 125 | 5 | 0.0071254 | 0.0473266 | macromolecule methylation |
| GO:0031328 | 918 | 17 | 0.0073053 | 0.0484157 | positive regulation of cellular biosynthetic process |
| GO:0007067 | 233 | 7 | 0.0073310 | 0.0484800 | mitotic nuclear division |
| GO:0009895 | 126 | 5 | 0.0073636 | 0.0485900 | negative regulation of catabolic process |
| GO:0030030 | 626 | 13 | 0.0074971 | 0.0493639 | cell projection organization |
| GO:0006283 | 42 | 3 | 0.0075562 | 0.0496460 | transcription-coupled nucleotide-excision repair |
| GO:0000165 | 127 | 5 | 0.0076072 | 0.0497682 | MAPK cascade |
| GO:0042177 | 81 | 4 | 0.0076593 | 0.0497682 | negative regulation of protein catabolic process |
| GO:0030855 | 235 | 7 | 0.0076668 | 0.0497682 | epithelial cell differentiation |
| GO:0030163 | 357 | 9 | 0.0076846 | 0.0497682 | protein catabolic process |
| GO:0021522 | 14 | 2 | 0.0077046 | 0.0497682 | spinal cord motor neuron differentiation |
| GO:0071825 | 14 | 2 | 0.0077046 | 0.0497682 | protein-lipid complex subunit organization |
| GO:0097061 | 14 | 2 | 0.0077046 | 0.0497682 | dendritic spine organization |
| GO:0045859 | 422 | 10 | 0.0077057 | 0.0497682 | regulation of protein kinase activity |
cc <- string_db$get_enrichment(hits$STRING_id,
category = "Component",
methodMT = "fdr", iea = TRUE ) %>%
dplyr::filter(pvalue_fdr < 0.05) %>%
tbl_df
cc %>% kable(.) %>%
kable_styling() %>%
scroll_box(width = "800px", height = "200px")| term_id | proteins | hits | pvalue | pvalue_fdr | term_description |
|---|---|---|---|---|---|
| GO:0005783 | 966 | 25 | 0.0000225 | 0.0085946 | endoplasmic reticulum |
| GO:0098588 | 1415 | 31 | 0.0000561 | 0.0102123 | bounding membrane of organelle |
| GO:0044432 | 677 | 19 | 0.0000802 | 0.0102123 | endoplasmic reticulum part |
| GO:0048471 | 429 | 14 | 0.0001556 | 0.0133113 | perinuclear region of cytoplasm |
| GO:0044459 | 1098 | 25 | 0.0001742 | 0.0133113 | plasma membrane part |
| GO:0045171 | 30 | 4 | 0.0002443 | 0.0155513 | intercellular bridge |
| GO:0005789 | 577 | 16 | 0.0003385 | 0.0174051 | endoplasmic reticulum membrane |
| GO:0042175 | 583 | 16 | 0.0003792 | 0.0174051 | nuclear outer membrane-endoplasmic reticulum membrane network |
| GO:0042995 | 1028 | 23 | 0.0004101 | 0.0174051 | cell projection |
| GO:0005635 | 273 | 10 | 0.0005636 | 0.0194581 | nuclear envelope |
| GO:0044454 | 225 | 9 | 0.0005669 | 0.0194581 | nuclear chromosome part |
| GO:0031226 | 671 | 17 | 0.0006192 | 0.0194581 | intrinsic component of plasma membrane |
| GO:0043005 | 554 | 15 | 0.0006622 | 0.0194581 | neuron projection |
| GO:0016607 | 144 | 7 | 0.0007497 | 0.0204556 | nuclear speck |
| GO:0044427 | 400 | 12 | 0.0009576 | 0.0239731 | chromosomal part |
| GO:0005887 | 641 | 16 | 0.0010440 | 0.0239731 | integral component of plasma membrane |
| GO:0000228 | 246 | 9 | 0.0010669 | 0.0239731 | nuclear chromosome |
| GO:0016604 | 252 | 9 | 0.0012617 | 0.0267751 | nuclear body |
| GO:0005730 | 603 | 15 | 0.0015425 | 0.0310120 | nucleolus |
| GO:0098796 | 546 | 14 | 0.0016645 | 0.0317918 | membrane protein complex |
| GO:0097458 | 686 | 16 | 0.0020861 | 0.0379468 | neuron part |
| GO:0005694 | 449 | 12 | 0.0025202 | 0.0437590 | chromosome |
mf <- string_db$get_enrichment(hits$STRING_id,
category = "Function",
methodMT = "fdr", iea = TRUE ) %>%
dplyr::filter(pvalue_fdr < 0.05) %>%
tbl_df
mf %>% kable(.) %>%
kable_styling() %>%
scroll_box(width = "800px", height = "200px")| term_id | proteins | hits | pvalue | pvalue_fdr | term_description |
|---|---|---|---|---|---|
| GO:0003677 | 1361 | 37 | 0.0000000 | 0.0000001 | DNA binding |
| GO:0016740 | 1373 | 36 | 0.0000000 | 0.0000003 | transferase activity |
| GO:0019899 | 881 | 25 | 0.0000001 | 0.0000204 | enzyme binding |
| GO:0032559 | 1054 | 27 | 0.0000003 | 0.0000308 | adenyl ribonucleotide binding |
| GO:0030554 | 1059 | 27 | 0.0000003 | 0.0000308 | adenyl nucleotide binding |
| GO:0016772 | 640 | 20 | 0.0000005 | 0.0000463 | transferase activity, transferring phosphorus-containing groups |
| GO:0005524 | 1031 | 26 | 0.0000006 | 0.0000463 | ATP binding |
| GO:0042802 | 597 | 19 | 0.0000008 | 0.0000483 | identical protein binding |
| GO:0032555 | 1263 | 29 | 0.0000008 | 0.0000483 | purine ribonucleotide binding |
| GO:0017076 | 1269 | 29 | 0.0000009 | 0.0000483 | purine nucleotide binding |
| GO:0032553 | 1272 | 29 | 0.0000010 | 0.0000483 | ribonucleotide binding |
| GO:0035639 | 1240 | 28 | 0.0000018 | 0.0000811 | purine ribonucleoside triphosphate binding |
| GO:0032550 | 1248 | 28 | 0.0000021 | 0.0000811 | purine ribonucleoside binding |
| GO:0001883 | 1251 | 28 | 0.0000022 | 0.0000811 | purine nucleoside binding |
| GO:0032549 | 1252 | 28 | 0.0000022 | 0.0000811 | ribonucleoside binding |
| GO:0001882 | 1256 | 28 | 0.0000023 | 0.0000811 | nucleoside binding |
| GO:0046914 | 891 | 22 | 0.0000066 | 0.0002148 | transition metal ion binding |
| GO:0097367 | 1419 | 29 | 0.0000082 | 0.0002532 | carbohydrate derivative binding |
| GO:0015075 | 390 | 13 | 0.0000289 | 0.0008454 | ion transmembrane transporter activity |
| GO:0022857 | 459 | 14 | 0.0000376 | 0.0010131 | transmembrane transporter activity |
| GO:0016301 | 521 | 15 | 0.0000383 | 0.0010131 | kinase activity |
| GO:0004674 | 300 | 11 | 0.0000516 | 0.0012563 | protein serine/threonine kinase activity |
| GO:0016773 | 473 | 14 | 0.0000521 | 0.0012563 | phosphotransferase activity, alcohol group as acceptor |
| GO:0004842 | 205 | 9 | 0.0000642 | 0.0014753 | ubiquitin-protein transferase activity |
| GO:0022891 | 423 | 13 | 0.0000665 | 0.0014753 | substrate-specific transmembrane transporter activity |
| GO:0000989 | 374 | 12 | 0.0000849 | 0.0018127 | transcription factor activity, transcription factor binding |
| GO:0019787 | 214 | 9 | 0.0000893 | 0.0018152 | ubiquitin-like protein transferase activity |
| GO:0000988 | 377 | 12 | 0.0000916 | 0.0018152 | transcription factor activity, protein binding |
| GO:0008270 | 769 | 18 | 0.0000950 | 0.0018172 | zinc ion binding |
| GO:0022892 | 510 | 14 | 0.0001157 | 0.0021404 | substrate-specific transporter activity |
| GO:0001071 | 580 | 15 | 0.0001271 | 0.0022049 | nucleic acid binding transcription factor activity |
| GO:0003700 | 580 | 15 | 0.0001271 | 0.0022049 | transcription factor activity, sequence-specific DNA binding |
| GO:0004672 | 396 | 12 | 0.0001451 | 0.0024093 | protein kinase activity |
| GO:0005088 | 94 | 6 | 0.0001476 | 0.0024093 | Ras guanyl-nucleotide exchange factor activity |
| GO:0005215 | 597 | 15 | 0.0001741 | 0.0027299 | transporter activity |
| GO:0019900 | 288 | 10 | 0.0001771 | 0.0027299 | kinase binding |
| GO:0003712 | 356 | 11 | 0.0002327 | 0.0034908 | transcription cofactor activity |
| GO:0015171 | 38 | 4 | 0.0002913 | 0.0042549 | amino acid transmembrane transporter activity |
| GO:0098772 | 703 | 16 | 0.0003217 | 0.0045773 | molecular function regulator |
| GO:0001047 | 71 | 5 | 0.0003386 | 0.0046979 | core promoter binding |
| GO:0019901 | 260 | 9 | 0.0003819 | 0.0051692 | protein kinase binding |
| GO:0003836 | 4 | 2 | 0.0004219 | 0.0055751 | beta-galactoside (CMP) alpha-2,3-sialyltransferase activity |
| GO:0061650 | 20 | 3 | 0.0006095 | 0.0078671 | ubiquitin-like protein conjugating enzyme activity |
| GO:0015174 | 5 | 2 | 0.0006993 | 0.0088201 | basic amino acid transmembrane transporter activity |
| GO:0003684 | 51 | 4 | 0.0009056 | 0.0111689 | damaged DNA binding |
| GO:0042605 | 6 | 2 | 0.0010430 | 0.0125846 | peptide antigen binding |
| GO:0003887 | 25 | 3 | 0.0011922 | 0.0137843 | DNA-directed DNA polymerase activity |
| GO:0034061 | 25 | 3 | 0.0011922 | 0.0137843 | DNA polymerase activity |
| GO:0044877 | 647 | 14 | 0.0012380 | 0.0138420 | macromolecular complex binding |
| GO:0019904 | 248 | 8 | 0.0012656 | 0.0138420 | protein domain specific binding |
| GO:0008324 | 308 | 9 | 0.0012720 | 0.0138420 | cation transmembrane transporter activity |
| GO:0016788 | 439 | 11 | 0.0013187 | 0.0140741 | hydrolase activity, acting on ester bonds |
| GO:0016787 | 1380 | 23 | 0.0013945 | 0.0146030 | hydrolase activity |
| GO:0016874 | 314 | 9 | 0.0014530 | 0.0149333 | ligase activity |
| GO:0015179 | 28 | 3 | 0.0016668 | 0.0168192 | L-amino acid transmembrane transporter activity |
| GO:0046943 | 61 | 4 | 0.0017712 | 0.0175543 | carboxylic acid transmembrane transporter activity |
| GO:0005342 | 62 | 4 | 0.0018811 | 0.0183156 | organic acid transmembrane transporter activity |
| GO:0061630 | 108 | 5 | 0.0022564 | 0.0215913 | ubiquitin protein ligase activity |
| GO:0061659 | 111 | 5 | 0.0025424 | 0.0239155 | ubiquitin-like protein ligase activity |
| GO:0046332 | 36 | 3 | 0.0034574 | 0.0319806 | SMAD binding |
| GO:0005085 | 122 | 5 | 0.0038182 | 0.0341793 | guanyl-nucleotide exchange factor activity |
| GO:0008509 | 122 | 5 | 0.0038182 | 0.0341793 | anion transmembrane transporter activity |
| GO:0003682 | 298 | 8 | 0.0039372 | 0.0346846 | chromatin binding |
| GO:0030674 | 78 | 4 | 0.0043333 | 0.0375776 | protein binding, bridging |
| GO:0031491 | 12 | 2 | 0.0044387 | 0.0378998 | nucleosome binding |
| GO:0008514 | 79 | 4 | 0.0045348 | 0.0381333 | organic anion transmembrane transporter activity |
| GO:0004536 | 40 | 3 | 0.0046675 | 0.0386640 | deoxyribonuclease activity |
| GO:0008187 | 13 | 2 | 0.0052167 | 0.0410795 | poly-pyrimidine tract binding |
| GO:0016628 | 13 | 2 | 0.0052167 | 0.0410795 | oxidoreductase activity, acting on the CH-CH group of donors, NAD or NADP as acceptor |
| GO:0005216 | 187 | 6 | 0.0052213 | 0.0410795 | ion channel activity |
| GO:0030234 | 526 | 11 | 0.0052552 | 0.0410795 | enzyme regulator activity |
| GO:0022838 | 190 | 6 | 0.0056347 | 0.0426682 | substrate-specific channel activity |
| GO:0022890 | 252 | 7 | 0.0057248 | 0.0426682 | inorganic cation transmembrane transporter activity |
| GO:0019200 | 14 | 2 | 0.0060525 | 0.0426682 | carbohydrate kinase activity |
| GO:0015267 | 194 | 6 | 0.0062225 | 0.0426682 | channel activity |
| GO:0022803 | 194 | 6 | 0.0062225 | 0.0426682 | passive transmembrane transporter activity |
| GO:0060090 | 91 | 4 | 0.0074616 | 0.0426682 | binding, bridging |
| GO:0003714 | 144 | 5 | 0.0076435 | 0.0426682 | transcription corepressor activity |
| GO:0005057 | 93 | 4 | 0.0080464 | 0.0426682 | receptor signaling protein activity |
| GO:0003777 | 49 | 3 | 0.0082351 | 0.0426682 | microtubule motor activity |
| GO:0005200 | 49 | 3 | 0.0082351 | 0.0426682 | structural constituent of cytoskeleton |
| GO:0001010 | 1 | 1 | 0.0084568 | 0.0426682 | transcription factor activity, sequence-specific DNA binding transcription factor recruiting |
| GO:0003882 | 1 | 1 | 0.0084568 | 0.0426682 | CDP-diacylglycerol-serine O-phosphatidyltransferase activity |
| GO:0004170 | 1 | 1 | 0.0084568 | 0.0426682 | dUTP diphosphatase activity |
| GO:0004499 | 1 | 1 | 0.0084568 | 0.0426682 | N,N-dimethylaniline monooxygenase activity |
| GO:0004632 | 1 | 1 | 0.0084568 | 0.0426682 | phosphopantothenate–cysteine ligase activity |
| GO:0004748 | 1 | 1 | 0.0084568 | 0.0426682 | ribonucleoside-diphosphate reductase activity, thioredoxin disulfide as acceptor |
| GO:0004808 | 1 | 1 | 0.0084568 | 0.0426682 | tRNA (5-methylaminomethyl-2-thiouridylate)-methyltransferase activity |
| GO:0008118 | 1 | 1 | 0.0084568 | 0.0426682 | N-acetyllactosaminide alpha-2,3-sialyltransferase activity |
| GO:0008482 | 1 | 1 | 0.0084568 | 0.0426682 | sulfite oxidase activity |
| GO:0015327 | 1 | 1 | 0.0084568 | 0.0426682 | cystine:glutamate antiporter activity |
| GO:0015328 | 1 | 1 | 0.0084568 | 0.0426682 | cystine secondary active transmembrane transporter activity |
| GO:0016728 | 1 | 1 | 0.0084568 | 0.0426682 | oxidoreductase activity, acting on CH or CH2 groups, disulfide as acceptor |
| GO:0030911 | 1 | 1 | 0.0084568 | 0.0426682 | TPR domain binding |
| GO:0033328 | 1 | 1 | 0.0084568 | 0.0426682 | peroxisome membrane targeting sequence binding |
| GO:0033858 | 1 | 1 | 0.0084568 | 0.0426682 | N-acetylgalactosamine kinase activity |
| GO:0033867 | 1 | 1 | 0.0084568 | 0.0426682 | Fas-activated serine/threonine kinase activity |
| GO:0033882 | 1 | 1 | 0.0084568 | 0.0426682 | choloyl-CoA hydrolase activity |
| GO:0034647 | 1 | 1 | 0.0084568 | 0.0426682 | histone demethylase activity (H3-trimethyl-K4 specific) |
| GO:0036105 | 1 | 1 | 0.0084568 | 0.0426682 | peroxisome membrane class-1 targeting sequence binding |
| GO:0043199 | 1 | 1 | 0.0084568 | 0.0426682 | sulfate binding |
| GO:0046811 | 1 | 1 | 0.0084568 | 0.0426682 | histone deacetylase inhibitor activity |
| GO:0046977 | 1 | 1 | 0.0084568 | 0.0426682 | TAP binding |
| GO:0047288 | 1 | 1 | 0.0084568 | 0.0426682 | monosialoganglioside sialyltransferase activity |
| GO:0048408 | 1 | 1 | 0.0084568 | 0.0426682 | epidermal growth factor binding |
| GO:0050613 | 1 | 1 | 0.0084568 | 0.0426682 | delta14-sterol reductase activity |
| GO:0052815 | 1 | 1 | 0.0084568 | 0.0426682 | medium-chain acyl-CoA hydrolase activity |
| GO:0061656 | 1 | 1 | 0.0084568 | 0.0426682 | SUMO conjugating enzyme activity |
| GO:0061731 | 1 | 1 | 0.0084568 | 0.0426682 | ribonucleoside-diphosphate reductase activity |
| GO:1901680 | 1 | 1 | 0.0084568 | 0.0426682 | sulfur-containing amino acid secondary active transmembrane transporter activity |
| GO:0046873 | 208 | 6 | 0.0086337 | 0.0429156 | metal ion transmembrane transporter activity |
| GO:0072509 | 95 | 4 | 0.0086605 | 0.0429156 | divalent inorganic cation transmembrane transporter activity |
| GO:0042803 | 342 | 8 | 0.0087981 | 0.0432121 | protein homodimerization activity |
| GO:0015035 | 17 | 2 | 0.0088964 | 0.0433114 | protein disulfide oxidoreductase activity |
| GO:0003723 | 1073 | 17 | 0.0095983 | 0.0463224 | RNA binding |
Cluster the pathways with PathCluster. This takes a lot of time…. Eval==F to skip this when knitting.
Fitted values extracted from DEXSeq, as DEXSeq identified DTU gene ZNF189
# Define genes
lab_genes <- c("ZNF189")
# Get transcript info from ensembl
genesToPlot <- DTU::get_gene_info(subset(obj$main_df$discovery$drim, gene_name %in% lab_genes)$tx_id, tx = T)
# Generate plots
plots1 <- DTU::plot_genes_cohort(obj = obj, cohort = "discovery", genes_toplot = genesToPlot, tool = "dex",
plot = F, only_nom_sig=F, want_jitter = F,
conditions = c("CT","PD")) ## [1] "extracting counts from the provided count object assuming it is a dex object"
## [1] "extracting counts from DEXSeq"
## [1] "extracting fitted couns from DEXSeq"
plots2 <- DTU::plot_genes_cohort(obj = obj, cohort = "replication", genes_toplot = genesToPlot,
tool = "dex", plot = F, only_nom_sig = F,
want_jitter = F, conditions = c("CT","PD")) ## [1] "extracting counts from the provided count object assuming it is a dex object"
## [1] "extracting counts from DEXSeq"
## [1] "extracting fitted couns from DEXSeq"
plots <- append(plots1,plots2)
# read qPCR results
znfLab <- read.csv(znfLabFile, sep = "\t") %>%
dplyr::select(tx_id, perc, condition, tx_biotype, sample_id)
colnames(znfLab) <- c("transcript_id", "frac", "condition", "tx_biotype", "sample_id")
znfLab %<>% dplyr::mutate(tx_id_label = (paste0(transcript_id, "\nprotein_coding"))) %>%
dplyr::mutate(countType = rep("qPCR", nrow(znfLab))) %>%
dplyr::mutate(condition = ifelse(condition == "CT", 0, 1))
# Extract counts from plot obj
dfs <- lapply(seq(1, length(plots)),function(i){
subset(plots[[i]]$data, sample_id %in% unique(znfLab$sample_id)) %>%
dplyr::select(transcript_id, sample_id, condition, frac, tx_id_label, countType)
})
# Filtered out transcript: "ENST00000496104" it is not expressed in replication
dfs[[1]] <- subset(dfs[[1]],transcript_id != "ENST00000496104")
dfs[[2]] <- subset(dfs[[2]],transcript_id != "ENST00000496104")
# Combine lab and insilico df
df <- gdata::combine(dfs[[1]], dfs[[2]]) %>%
dplyr::select(transcript_id, frac, condition, tx_id_label, countType)
znfLab %<>% dplyr::select(transcript_id, frac, condition, tx_id_label, countType)
df <- gdata::combine(df, znfLab, names=c("RNASeq","qPCR")) %>% dplyr::filter(!grepl("dge", countType))
# plot function
makeLabPlot <-function(df, tool, tag, legend = F) {
p <- ggplot(subset(df, countType == "qPCR" | countType == "observed_tx"),
aes(x = condition, y = frac)) +
geom_jitter(position = position_jitter(0.1), size = 1.5) +
stat_summary(fun.y = median, geom = "errorbar", aes(ymax = ..y.., ymin = ..y..,col="red"),
width = .75, linetype = "dashed") +
stat_summary(fun.y = median, colour="red", geom="line", aes(group = 1)) +
facet_grid(cols = vars(tx_id_label), rows = vars(source), scales = "free_y") +
geom_boxplot(data = subset(df, countType == "fitted_tx") %>%
dplyr::group_by(condition, transcript_id) %>%
dplyr::mutate(mean = median(frac)),
aes(x = condition, y = mean, col = "blue"),
inherit.aes = F, size = 0.2) +
labs(x = "Condition", y = "Relative abundance",
title = "", tag = tag, col = "Median of: ") +
theme_bw() +
scale_x_discrete(labels = c("0" = "CT", "1" = "PD")) +
scale_color_manual(values = c("red" = "red", "blue" = "blue"),
labels = c("red" = "observed values\n (black points)",
"blue" = paste0("fitted values - ", tool, " \n (points not displayed)"))) +
theme(panel.spacing = unit(1, "lines")) +
theme(strip.background = element_rect(fill = "black"))+
theme(strip.text = element_text(color = "white", face = "bold"))
if (legend) {
p <- p + theme(legend.position = "bottom")
} else {
p <- p + theme(legend.position = "none")
}
return(p)
}
# Make the plot
znf <- makeLabPlot(df = df, tool = "DEXSeq", tag = "")
znf## png
## 2
## png
## 2
disc_drim <- obj$main_df$discovery$drim %>%
dplyr::select(-rankDex, -toolAdjPval) %>%
dplyr::filter(!is.na(gene_pvalueStageR)) %>%
dplyr::arrange(gene_name)
disc_dex <- obj$main_df$discovery$dex %>%
dplyr::select(-rankDrim, -toolAdjPval) %>%
dplyr::filter(!is.na(gene_pvalueStageR)) %>%
dplyr::arrange(gene_name)
repl_drim <- obj$main_df$replication$drim %>%
dplyr::select(-rankDex, -toolAdjPval) %>%
dplyr::filter(!is.na(gene_pvalueStageR)) %>%
dplyr::arrange(gene_name)
repl_dex <- obj$main_df$replication$dex %>%
dplyr::select(-rankDrim, -toolAdjPval) %>%
dplyr::filter(!is.na(gene_pvalueStageR)) %>%
dplyr::arrange(gene_name)
disc <- dplyr::bind_rows("DRIMSeq" = disc_drim, "DEXSeq" = disc_dex, .id = "tool")
repl <- dplyr::bind_rows("DRIMSeq" = repl_drim, "DEXSeq" = repl_dex, .id = "tool")
disc %>% kable(.) %>%
kable_styling() %>%
scroll_box(width = "800px", height = "200px")| tool | tx_id | gene_pvalueStageR | tx_pvalueStageR | nom_pval | gene_id | gene_name | tx_biotype | l2fc |
|---|---|---|---|---|---|---|---|---|
| DRIMSeq | ENST00000464157 | 0.0009145 | 0.0000098 | 0.0000004 | ENSG00000107331 | ABCA2 | processed_transcript | 1.8203240 |
| DRIMSeq | ENST00000428549 | 0.0071572 | 0.0314952 | 0.0004393 | ENSG00000141338 | ABCA8 | retained_intron | 1.0576213 |
| DRIMSeq | ENST00000280560 | 0.0110404 | 0.0002220 | 0.0000023 | ENSG00000150967 | ABCB9 | protein_coding | -2.6782652 |
| DRIMSeq | ENST00000442687 | 0.0495117 | 0.0000000 | 0.0020474 | ENSG00000239642 | AC034228.7 | transcribed_unprocessed_pseudogene | -1.5713896 |
| DRIMSeq | ENST00000446743 | 0.0495117 | 0.0000000 | 0.0020474 | ENSG00000239642 | AC034228.7 | processed_transcript | 1.5713896 |
| DRIMSeq | ENST00000430844 | 0.0440606 | 0.0082266 | 0.0003443 | ENSG00000228010 | AC073343.13 | antisense | -1.0155638 |
| DRIMSeq | ENST00000497320 | 0.0199445 | 0.0065538 | 0.0002743 | ENSG00000242474 | AC093627.9 | lincRNA | -1.1730599 |
| DRIMSeq | ENST00000452171 | 0.0154020 | 0.0336502 | 0.0007041 | ENSG00000060971 | ACAA1 | protein_coding | -1.2643208 |
| DRIMSeq | ENST00000350303 | 0.0388816 | 0.0057169 | 0.0000797 | ENSG00000072778 | ACADVL | protein_coding | -1.3504959 |
| DRIMSeq | ENST00000379923 | 0.0240217 | 0.0023476 | 0.0000982 | ENSG00000122729 | ACO1 | protein_coding | -1.3784695 |
| DRIMSeq | ENST00000217455 | 0.0348237 | 0.0000000 | 0.0010323 | ENSG00000101473 | ACOT8 | protein_coding | -0.9326298 |
| DRIMSeq | ENST00000484975 | 0.0348237 | 0.0000000 | 0.0010323 | ENSG00000101473 | ACOT8 | retained_intron | 0.9326298 |
| DRIMSeq | ENST00000160382 | 0.0370298 | 0.0048993 | 0.0001025 | ENSG00000077080 | ACTL6B | protein_coding | -0.8918091 |
| DRIMSeq | ENST00000271836 | 0.0420729 | 0.0079299 | 0.0001659 | ENSG00000143537 | ADAM15 | protein_coding | -1.5311314 |
| DRIMSeq | ENST00000381312 | 0.0488893 | 0.0293910 | 0.0006150 | ENSG00000185736 | ADARB2 | protein_coding | -0.8717468 |
| DRIMSeq | ENST00000373443 | 0.0151134 | 0.0005682 | 0.0000079 | ENSG00000142920 | ADC | protein_coding | -1.8158726 |
| DRIMSeq | ENST00000285518 | 0.0496424 | 0.0000000 | 0.0020630 | ENSG00000155189 | AGPAT5 | protein_coding | -0.8790660 |
| DRIMSeq | ENST00000530716 | 0.0496424 | 0.0000000 | 0.0020630 | ENSG00000155189 | AGPAT5 | processed_transcript | 0.8790660 |
| DRIMSeq | ENST00000475985 | 0.0114150 | 0.0028440 | 0.0000595 | ENSG00000117448 | AKR1A1 | processed_transcript | 1.5196852 |
| DRIMSeq | ENST00000407796 | 0.0154087 | 0.0000000 | 0.0002420 | ENSG00000142208 | AKT1 | protein_coding | -1.1873011 |
| DRIMSeq | ENST00000555380 | 0.0154087 | 0.0000000 | 0.0002420 | ENSG00000142208 | AKT1 | protein_coding | 1.1873011 |
| DRIMSeq | ENST00000344175 | 0.0061001 | 0.0000332 | 0.0000005 | ENSG00000204673 | AKT1S1 | protein_coding | -1.8242347 |
| DRIMSeq | ENST00000394458 | 0.0232151 | 0.0000000 | 0.0004974 | ENSG00000160117 | ANKLE1 | protein_coding | 1.4685539 |
| DRIMSeq | ENST00000404085 | 0.0232151 | 0.0000000 | 0.0004974 | ENSG00000160117 | ANKLE1 | protein_coding | -1.4685539 |
| DRIMSeq | ENST00000307518 | 0.0277435 | 0.0190510 | 0.0007972 | ENSG00000165887 | ANKRD2 | protein_coding | 3.6848343 |
| DRIMSeq | ENST00000265748 | 0.0020017 | 0.0002783 | 0.0000116 | ENSG00000011426 | ANLN | protein_coding | -1.4866235 |
| DRIMSeq | ENST00000441696 | 0.0020017 | 0.0363081 | 0.0015194 | ENSG00000011426 | ANLN | nonsense_mediated_decay | 1.5410206 |
| DRIMSeq | ENST00000597643 | 0.0151134 | 0.0000000 | 0.0002282 | ENSG00000074855 | ANO8 | nonsense_mediated_decay | 1.2195595 |
| DRIMSeq | ENST00000159087 | 0.0151134 | 0.0000000 | 0.0002282 | ENSG00000074855 | ANO8 | protein_coding | -1.2195595 |
| DRIMSeq | ENST00000394295 | 0.0215993 | 0.0082736 | 0.0001731 | ENSG00000196975 | ANXA4 | protein_coding | -0.8072394 |
| DRIMSeq | ENST00000336418 | 0.0456265 | 0.0000000 | 0.0017366 | ENSG00000157823 | AP3S2 | protein_coding | 3.0522100 |
| DRIMSeq | ENST00000560940 | 0.0456265 | 0.0000000 | 0.0017366 | ENSG00000157823 | AP3S2 | protein_coding | -3.0522100 |
| DRIMSeq | ENST00000527830 | 0.0440348 | 0.0069459 | 0.0002907 | ENSG00000149089 | APIP | processed_transcript | -2.8756330 |
| DRIMSeq | ENST00000447138 | 0.0140365 | 0.0000000 | 0.0001987 | ENSG00000101474 | APMAP | protein_coding | -1.3020439 |
| DRIMSeq | ENST00000217456 | 0.0140365 | 0.0000000 | 0.0001987 | ENSG00000101474 | APMAP | protein_coding | 1.3020439 |
| DRIMSeq | ENST00000426324 | 0.0302169 | 0.0060117 | 0.0002516 | ENSG00000198931 | APRT | protein_coding | -1.1216256 |
| DRIMSeq | ENST00000426335 | 0.0154087 | 0.0000000 | 0.0002412 | ENSG00000149182 | ARFGAP2 | protein_coding | 1.0012903 |
| DRIMSeq | ENST00000524782 | 0.0154087 | 0.0000000 | 0.0002412 | ENSG00000149182 | ARFGAP2 | protein_coding | -1.0012903 |
| DRIMSeq | ENST00000582520 | 0.0232151 | 0.0115668 | 0.0001613 | ENSG00000141522 | ARHGDIA | processed_transcript | 2.0332131 |
| DRIMSeq | ENST00000452522 | 0.0337902 | 0.0096816 | 0.0004051 | ENSG00000074964 | ARHGEF10L | protein_coding | -1.0385160 |
| DRIMSeq | ENST00000541725 | 0.0396600 | 0.0221211 | 0.0003086 | ENSG00000105676 | ARMC6 | protein_coding | 1.9490360 |
| DRIMSeq | ENST00000494015 | 0.0388082 | 0.0050847 | 0.0002128 | ENSG00000114098 | ARMC8 | retained_intron | 1.7739126 |
| DRIMSeq | ENST00000374007 | 0.0240060 | 0.0000000 | 0.0005422 | ENSG00000204147 | ASAH2B | protein_coding | -0.9347490 |
| DRIMSeq | ENST00000185907 | 0.0240060 | 0.0000000 | 0.0005422 | ENSG00000204147 | ASAH2B | protein_coding | 0.9347490 |
| DRIMSeq | ENST00000380920 | 0.0471741 | 0.0105085 | 0.0004397 | ENSG00000141505 | ASGR1 | protein_coding | -1.5775702 |
| DRIMSeq | ENST00000554151 | 0.0130174 | 0.0023241 | 0.0000486 | ENSG00000066739 | ATG2B | processed_transcript | 0.9814713 |
| DRIMSeq | ENST00000359933 | 0.0130174 | 0.0100159 | 0.0002096 | ENSG00000066739 | ATG2B | protein_coding | -0.7504442 |
| DRIMSeq | ENST00000557311 | 0.0065356 | 0.0002934 | 0.0000041 | ENSG00000066427 | ATXN3 | protein_coding | -1.5790737 |
| DRIMSeq | ENST00000377526 | 0.0141822 | 0.0007264 | 0.0000304 | ENSG00000115307 | AUP1 | protein_coding | -1.1043431 |
| DRIMSeq | ENST00000570947 | 0.0005260 | 0.0000184 | 0.0000004 | ENSG00000175711 | B3GNTL1 | processed_transcript | 4.7808994 |
| DRIMSeq | ENST00000261499 | 0.0094813 | 0.0040775 | 0.0000569 | ENSG00000108641 | B9D1 | protein_coding | -1.0057055 |
| DRIMSeq | ENST00000369541 | 0.0456265 | 0.0000000 | 0.0017278 | ENSG00000116752 | BCAS2 | protein_coding | -0.9433829 |
| DRIMSeq | ENST00000485021 | 0.0456265 | 0.0000000 | 0.0017278 | ENSG00000116752 | BCAS2 | processed_transcript | 0.9433829 |
| DRIMSeq | ENST00000264381 | 0.0140365 | 0.0000000 | 0.0001977 | ENSG00000114200 | BCHE | protein_coding | -1.8140288 |
| DRIMSeq | ENST00000540653 | 0.0140365 | 0.0000000 | 0.0001977 | ENSG00000114200 | BCHE | protein_coding | 1.8140288 |
| DRIMSeq | ENST00000409400 | 0.0078481 | 0.0009747 | 0.0000136 | ENSG00000136717 | BIN1 | protein_coding | -1.2746670 |
| DRIMSeq | ENST00000423798 | 0.0391529 | 0.0117334 | 0.0002455 | ENSG00000137274 | BPHL | protein_coding | 1.7326422 |
| DRIMSeq | ENST00000583624 | 0.0186052 | 0.0129380 | 0.0002707 | ENSG00000005379 | BZRAP1 | retained_intron | 0.7665831 |
| DRIMSeq | ENST00000533472 | 0.0212969 | 0.0019594 | 0.0000820 | ENSG00000182993 | C12orf60 | processed_transcript | 1.0125358 |
| DRIMSeq | ENST00000342683 | 0.0170550 | 0.0028686 | 0.0001200 | ENSG00000189227 | C15orf61 | protein_coding | 1.1658347 |
| DRIMSeq | ENST00000338401 | 0.0017975 | 0.0000622 | 0.0000026 | ENSG00000130731 | C16orf13 | protein_coding | 1.2247350 |
| DRIMSeq | ENST00000397666 | 0.0017975 | 0.0299636 | 0.0012539 | ENSG00000130731 | C16orf13 | protein_coding | -0.8010465 |
| DRIMSeq | ENST00000459925 | 0.0470082 | 0.0000000 | 0.0018435 | ENSG00000159761 | C16orf86 | retained_intron | 1.5924318 |
| DRIMSeq | ENST00000403458 | 0.0470082 | 0.0000000 | 0.0018435 | ENSG00000159761 | C16orf86 | protein_coding | -1.5924318 |
| DRIMSeq | ENST00000565112 | 0.0372295 | 0.0075303 | 0.0003151 | ENSG00000155330 | C16orf87 | protein_coding | 1.0567511 |
| DRIMSeq | ENST00000588730 | 0.0286343 | 0.0017239 | 0.0000361 | ENSG00000152242 | C18orf25 | protein_coding | -1.6718541 |
| DRIMSeq | ENST00000294360 | 0.0008174 | 0.0000015 | 0.0000000 | ENSG00000162384 | C1orf123 | protein_coding | -1.0364800 |
| DRIMSeq | ENST00000493514 | 0.0010311 | 0.0000110 | 0.0000002 | ENSG00000162642 | C1orf52 | processed_transcript | -3.6963932 |
| DRIMSeq | ENST00000243189 | 0.0162533 | 0.0456796 | 0.0006372 | ENSG00000117616 | C1orf63 | protein_coding | 1.1304880 |
| DRIMSeq | ENST00000419612 | 0.0114729 | 0.0011603 | 0.0000243 | ENSG00000197183 | C20orf112 | protein_coding | 1.0574955 |
| DRIMSeq | ENST00000436325 | 0.0486374 | 0.0362970 | 0.0015189 | ENSG00000188315 | C3orf62 | protein_coding | 1.1134020 |
| DRIMSeq | ENST00000300900 | 0.0108473 | 0.0018686 | 0.0000261 | ENSG00000167434 | CA4 | protein_coding | -1.0491591 |
| DRIMSeq | ENST00000277549 | 0.0257168 | 0.0007590 | 0.0000079 | ENSG00000148408 | CACNA1B | protein_coding | -0.8841895 |
| DRIMSeq | ENST00000539935 | 0.0319243 | 0.0160198 | 0.0002235 | ENSG00000182389 | CACNB4 | protein_coding | -0.6497330 |
| DRIMSeq | ENST00000383710 | 0.0006675 | 0.0334416 | 0.0004665 | ENSG00000163618 | CADPS | protein_coding | -0.6596552 |
| DRIMSeq | ENST00000462768 | 0.0006675 | 0.0359395 | 0.0005013 | ENSG00000163618 | CADPS | processed_transcript | 0.8965756 |
| DRIMSeq | ENST00000550804 | 0.0006603 | 0.0000013 | 0.0000000 | ENSG00000012822 | CALCOCO1 | protein_coding | -0.9453936 |
| DRIMSeq | ENST00000333868 | 0.0407671 | 0.0209520 | 0.0004384 | ENSG00000132906 | CASP9 | protein_coding | -0.9396896 |
| DRIMSeq | ENST00000562719 | 0.0328170 | 0.0492656 | 0.0010308 | ENSG00000129993 | CBFA2T3 | protein_coding | 1.4338801 |
| DRIMSeq | ENST00000464832 | 0.0042411 | 0.0000162 | 0.0000002 | ENSG00000128596 | CCDC136 | protein_coding | -0.9917716 |
| DRIMSeq | ENST00000588821 | 0.0010311 | 0.0000379 | 0.0000008 | ENSG00000183401 | CCDC159 | retained_intron | 2.3549713 |
| DRIMSeq | ENST00000538586 | 0.0454731 | 0.0188191 | 0.0002625 | ENSG00000123106 | CCDC91 | protein_coding | 0.8028450 |
| DRIMSeq | ENST00000300415 | 0.0373939 | 0.0000000 | 0.0011541 | ENSG00000101331 | CCM2L | protein_coding | 2.2650169 |
| DRIMSeq | ENST00000452892 | 0.0373939 | 0.0000000 | 0.0011541 | ENSG00000101331 | CCM2L | protein_coding | -2.2650169 |
| DRIMSeq | ENST00000513102 | 0.0131100 | 0.0011948 | 0.0000500 | ENSG00000134057 | CCNB1 | retained_intron | 1.9251654 |
| DRIMSeq | ENST00000305596 | 0.0287317 | 0.0000000 | 0.0007519 | ENSG00000169217 | CD2BP2 | protein_coding | 1.1378188 |
| DRIMSeq | ENST00000569466 | 0.0287317 | 0.0000000 | 0.0007519 | ENSG00000169217 | CD2BP2 | protein_coding | -1.1378188 |
| DRIMSeq | ENST00000367041 | 0.0153421 | 0.0016072 | 0.0000336 | ENSG00000117335 | CD46 | protein_coding | -1.2505353 |
| DRIMSeq | ENST00000476153 | 0.0495117 | 0.0300290 | 0.0006283 | ENSG00000117266 | CDK18 | retained_intron | 1.0544479 |
| DRIMSeq | ENST00000346416 | 0.0099566 | 0.0008745 | 0.0000183 | ENSG00000101391 | CDK5RAP1 | protein_coding | -0.9271653 |
| DRIMSeq | ENST00000399837 | 0.0283962 | 0.0168402 | 0.0007047 | ENSG00000093072 | CECR1 | protein_coding | -1.9283406 |
| DRIMSeq | ENST00000514507 | 0.0068260 | 0.0002572 | 0.0000108 | ENSG00000112877 | CEP72 | processed_transcript | 1.0873366 |
| DRIMSeq | ENST00000262450 | 0.0039202 | 0.0000000 | 0.0000241 | ENSG00000116254 | CHD5 | protein_coding | 1.4686656 |
| DRIMSeq | ENST00000378021 | 0.0039202 | 0.0000000 | 0.0000241 | ENSG00000116254 | CHD5 | protein_coding | -1.4686656 |
| DRIMSeq | ENST00000255409 | 0.0168681 | 0.0010098 | 0.0000423 | ENSG00000133048 | CHI3L1 | protein_coding | -1.0521000 |
| DRIMSeq | ENST00000472064 | 0.0168681 | 0.0416564 | 0.0017432 | ENSG00000133048 | CHI3L1 | retained_intron | 1.0780159 |
| DRIMSeq | ENST00000325167 | 0.0036548 | 0.0000817 | 0.0000034 | ENSG00000176108 | CHMP6 | protein_coding | -1.3945507 |
| DRIMSeq | ENST00000258930 | 0.0328170 | 0.0000000 | 0.0009530 | ENSG00000136425 | CIB2 | protein_coding | -1.6091430 |
| DRIMSeq | ENST00000560618 | 0.0328170 | 0.0000000 | 0.0009530 | ENSG00000136425 | CIB2 | protein_coding | 1.6091430 |
| DRIMSeq | ENST00000424691 | 0.0456265 | 0.0037102 | 0.0000776 | ENSG00000186162 | CIDECP | processed_transcript | -0.8296886 |
| DRIMSeq | ENST00000216756 | 0.0031937 | 0.0001535 | 0.0000064 | ENSG00000100865 | CINP | protein_coding | -1.0206448 |
| DRIMSeq | ENST00000296951 | 0.0098169 | 0.0000000 | 0.0001010 | ENSG00000113282 | CLINT1 | protein_coding | 1.8890660 |
| DRIMSeq | ENST00000411809 | 0.0098169 | 0.0000000 | 0.0001010 | ENSG00000113282 | CLINT1 | protein_coding | -1.8890660 |
| DRIMSeq | ENST00000568865 | 0.0471741 | 0.0107545 | 0.0004500 | ENSG00000064666 | CNN2 | protein_coding | -1.6092766 |
| DRIMSeq | ENST00000517876 | 0.0257168 | 0.0000000 | 0.0006206 | ENSG00000155508 | CNOT8 | protein_coding | 1.0590803 |
| DRIMSeq | ENST00000285896 | 0.0257168 | 0.0000000 | 0.0006206 | ENSG00000155508 | CNOT8 | protein_coding | -1.0590803 |
| DRIMSeq | ENST00000548013 | 0.0391529 | 0.0085603 | 0.0001194 | ENSG00000257727 | CNPY2 | retained_intron | -0.7921687 |
| DRIMSeq | ENST00000459895 | 0.0071631 | 0.0212707 | 0.0004451 | ENSG00000182871 | COL18A1 | processed_transcript | -1.7248831 |
| DRIMSeq | ENST00000462604 | 0.0000001 | 0.0000000 | 0.0000000 | ENSG00000144810 | COL8A1 | processed_transcript | 8.3837880 |
| DRIMSeq | ENST00000444869 | 0.0196447 | 0.0071465 | 0.0001495 | ENSG00000148444 | COMMD3 | protein_coding | 2.5495677 |
| DRIMSeq | ENST00000267935 | 0.0011638 | 0.0004655 | 0.0000049 | ENSG00000140365 | COMMD4 | protein_coding | -1.1523673 |
| DRIMSeq | ENST00000567935 | 0.0011638 | 0.0358820 | 0.0003754 | ENSG00000140365 | COMMD4 | retained_intron | 0.9626023 |
| DRIMSeq | ENST00000249923 | 0.0398942 | 0.0000000 | 0.0013609 | ENSG00000129083 | COPB1 | protein_coding | 0.8482051 |
| DRIMSeq | ENST00000439561 | 0.0398942 | 0.0000000 | 0.0013609 | ENSG00000129083 | COPB1 | protein_coding | -0.8482051 |
| DRIMSeq | ENST00000251166 | 0.0313144 | 0.0047380 | 0.0001983 | ENSG00000262246 | CORO7 | protein_coding | -1.0169368 |
| DRIMSeq | ENST00000377049 | 0.0415266 | 0.0000000 | 0.0014864 | ENSG00000241563 | CORT | protein_coding | 1.7654900 |
| DRIMSeq | ENST00000320498 | 0.0415266 | 0.0000000 | 0.0014864 | ENSG00000241563 | CORT | protein_coding | -1.7654900 |
| DRIMSeq | ENST00000299335 | 0.0291518 | 0.0073175 | 0.0001531 | ENSG00000166260 | COX11 | protein_coding | -0.7270948 |
| DRIMSeq | ENST00000382395 | 0.0183958 | 0.0011899 | 0.0000249 | ENSG00000137449 | CPEB2 | protein_coding | -0.8246696 |
| DRIMSeq | ENST00000414664 | 0.0248575 | 0.0365076 | 0.0007639 | ENSG00000214078 | CPNE1 | protein_coding | -0.7967470 |
| DRIMSeq | ENST00000493411 | 0.0398035 | 0.0000000 | 0.0013418 | ENSG00000124772 | CPNE5 | processed_transcript | 0.9949214 |
| DRIMSeq | ENST00000244751 | 0.0398035 | 0.0000000 | 0.0013418 | ENSG00000124772 | CPNE5 | protein_coding | -0.9949214 |
| DRIMSeq | ENST00000435064 | 0.0406755 | 0.0075934 | 0.0003178 | ENSG00000127054 | CPSF3L | protein_coding | -0.8056608 |
| DRIMSeq | ENST00000332896 | 0.0188736 | 0.0038930 | 0.0000543 | ENSG00000169372 | CRADD | protein_coding | -1.1599359 |
| DRIMSeq | ENST00000452070 | 0.0036548 | 0.0330428 | 0.0004609 | ENSG00000163703 | CRELD1 | protein_coding | -1.2337124 |
| DRIMSeq | ENST00000589066 | 0.0143661 | 0.0000000 | 0.0002100 | ENSG00000267011 | CTB-50L17.16 | lincRNA | -2.0711939 |
| DRIMSeq | ENST00000591414 | 0.0143661 | 0.0000000 | 0.0002100 | ENSG00000267011 | CTB-50L17.16 | lincRNA | 2.0711939 |
| DRIMSeq | ENST00000412431 | 0.0475025 | 0.0000000 | 0.0019101 | ENSG00000230551 | CTB-89H12.4 | processed_transcript | -1.7884104 |
| DRIMSeq | ENST00000499521 | 0.0475025 | 0.0000000 | 0.0019101 | ENSG00000230551 | CTB-89H12.4 | retained_intron | 1.7884104 |
| DRIMSeq | ENST00000415461 | 0.0093571 | 0.0004165 | 0.0000174 | ENSG00000085733 | CTTN | protein_coding | 1.1090384 |
| DRIMSeq | ENST00000478630 | 0.0329283 | 0.0054399 | 0.0002276 | ENSG00000044090 | CUL7 | processed_transcript | 1.1090923 |
| DRIMSeq | ENST00000490926 | 0.0169822 | 0.0068615 | 0.0002871 | ENSG00000114395 | CYB561D2 | processed_transcript | 1.4042158 |
| DRIMSeq | ENST00000252945 | 0.0437751 | 0.0445079 | 0.0009313 | ENSG00000130649 | CYP2E1 | protein_coding | -1.2988260 |
| DRIMSeq | ENST00000368336 | 0.0036630 | 0.0000000 | 0.0000221 | ENSG00000132676 | DAP3 | protein_coding | -2.0827624 |
| DRIMSeq | ENST00000491777 | 0.0036630 | 0.0000000 | 0.0000221 | ENSG00000132676 | DAP3 | protein_coding | 2.0827624 |
| DRIMSeq | ENST00000301264 | 0.0226004 | 0.0043572 | 0.0001823 | ENSG00000167657 | DAPK3 | protein_coding | -0.7744343 |
| DRIMSeq | ENST00000233078 | 0.0049043 | 0.0001506 | 0.0000021 | ENSG00000071626 | DAZAP1 | protein_coding | -1.0834022 |
| DRIMSeq | ENST00000471767 | 0.0125518 | 0.0008924 | 0.0000373 | ENSG00000113758 | DBN1 | retained_intron | 1.3438272 |
| DRIMSeq | ENST00000220764 | 0.0002283 | 0.0000013 | 0.0000001 | ENSG00000104325 | DECR1 | protein_coding | -1.3752789 |
| DRIMSeq | ENST00000521668 | 0.0002283 | 0.0042333 | 0.0001772 | ENSG00000104325 | DECR1 | processed_transcript | 1.2559800 |
| DRIMSeq | ENST00000537639 | 0.0001595 | 0.0000005 | 0.0000000 | ENSG00000146966 | DENND2A | protein_coding | -3.3281245 |
| DRIMSeq | ENST00000485359 | 0.0111878 | 0.0029746 | 0.0001245 | ENSG00000198837 | DENND4B | retained_intron | 1.0039172 |
| DRIMSeq | ENST00000559656 | 0.0162533 | 0.0061220 | 0.0001281 | ENSG00000140543 | DET1 | processed_transcript | 2.4857970 |
| DRIMSeq | ENST00000409775 | 0.0000646 | 0.0000001 | 0.0000000 | ENSG00000105928 | DFNA5 | protein_coding | -1.7267904 |
| DRIMSeq | ENST00000331444 | 0.0098938 | 0.0005608 | 0.0000078 | ENSG00000183628 | DGCR6 | protein_coding | -1.1725661 |
| DRIMSeq | ENST00000497151 | 0.0077076 | 0.0020062 | 0.0000210 | ENSG00000102796 | DHRS12 | processed_transcript | 1.3640151 |
| DRIMSeq | ENST00000437541 | 0.0061001 | 0.0001099 | 0.0000023 | ENSG00000231764 | DLX6-AS1 | antisense | 1.7689443 |
| DRIMSeq | ENST00000592152 | 0.0078481 | 0.0036805 | 0.0000513 | ENSG00000187775 | DNAH17 | processed_transcript | -1.7930853 |
| DRIMSeq | ENST00000473051 | 0.0248575 | 0.0203178 | 0.0004251 | ENSG00000148719 | DNAJB12 | retained_intron | 0.9263625 |
| DRIMSeq | ENST00000379263 | 0.0169973 | 0.0473923 | 0.0004958 | ENSG00000105821 | DNAJC2 | protein_coding | -0.6414625 |
| DRIMSeq | ENST00000463668 | 0.0440348 | 0.0084165 | 0.0003522 | ENSG00000142197 | DOPEY2 | retained_intron | 0.7423597 |
| DRIMSeq | ENST00000561411 | 0.0003707 | 0.0051592 | 0.0000720 | ENSG00000134146 | DPH6 | protein_coding | -1.7862415 |
| DRIMSeq | ENST00000559585 | 0.0003707 | 0.0195683 | 0.0002730 | ENSG00000134146 | DPH6 | processed_transcript | -1.2947856 |
| DRIMSeq | ENST00000314392 | 0.0408566 | 0.0347709 | 0.0014551 | ENSG00000136908 | DPM2 | protein_coding | -0.8318632 |
| DRIMSeq | ENST00000360510 | 0.0066714 | 0.0001228 | 0.0000017 | ENSG00000254986 | DPP3 | protein_coding | -2.4786956 |
| DRIMSeq | ENST00000561350 | 0.0000060 | 0.0000000 | 0.0000000 | ENSG00000128951 | DUT | processed_transcript | 1.6823046 |
| DRIMSeq | ENST00000558813 | 0.0000060 | 0.0002405 | 0.0000101 | ENSG00000128951 | DUT | protein_coding | -0.8812886 |
| DRIMSeq | ENST00000379378 | 0.0378375 | 0.0067078 | 0.0002807 | ENSG00000205250 | E2F4 | protein_coding | -0.8668229 |
| DRIMSeq | ENST00000610011 | 0.0486374 | 0.0072775 | 0.0003045 | ENSG00000249786 | EAF1-AS1 | antisense | 2.7866400 |
| DRIMSeq | ENST00000342725 | 0.0000133 | 0.0000000 | 0.0000000 | ENSG00000088881 | EBF4 | protein_coding | -2.9289960 |
| DRIMSeq | ENST00000415912 | 0.0398035 | 0.0000000 | 0.0013495 | ENSG00000117298 | ECE1 | protein_coding | -1.1233416 |
| DRIMSeq | ENST00000470394 | 0.0398035 | 0.0000000 | 0.0013495 | ENSG00000117298 | ECE1 | retained_intron | 1.1233416 |
| DRIMSeq | ENST00000562238 | 0.0029802 | 0.0301363 | 0.0006306 | ENSG00000167969 | ECI1 | protein_coding | -0.9019361 |
| DRIMSeq | ENST00000565326 | 0.0221559 | 0.0019507 | 0.0000408 | ENSG00000197774 | EME2 | retained_intron | 2.4087661 |
| DRIMSeq | ENST00000562277 | 0.0066668 | 0.0001557 | 0.0000065 | ENSG00000196678 | ERI2 | processed_transcript | 3.9304830 |
| DRIMSeq | ENST00000468103 | 0.0019586 | 0.0000445 | 0.0000009 | ENSG00000158220 | ESYT3 | retained_intron | 0.9048475 |
| DRIMSeq | ENST00000306376 | 0.0348861 | 0.0000000 | 0.0010389 | ENSG00000244405 | ETV5 | protein_coding | -1.1139139 |
| DRIMSeq | ENST00000475484 | 0.0348861 | 0.0000000 | 0.0010389 | ENSG00000244405 | ETV5 | retained_intron | 1.1139139 |
| DRIMSeq | ENST00000512944 | 0.0392781 | 0.0000000 | 0.0012973 | ENSG00000180104 | EXOC3 | protein_coding | -2.1749415 |
| DRIMSeq | ENST00000315013 | 0.0392781 | 0.0000000 | 0.0012973 | ENSG00000180104 | EXOC3 | protein_coding | 2.1749415 |
| DRIMSeq | ENST00000374280 | 0.0026086 | 0.0000425 | 0.0000018 | ENSG00000158008 | EXTL1 | protein_coding | -1.0683296 |
| DRIMSeq | ENST00000470037 | 0.0026086 | 0.0026405 | 0.0001105 | ENSG00000158008 | EXTL1 | processed_transcript | 1.0021763 |
| DRIMSeq | ENST00000428826 | 0.0271797 | 0.0069012 | 0.0002888 | ENSG00000108799 | EZH1 | protein_coding | -0.7911486 |
| DRIMSeq | ENST00000586714 | 0.0271797 | 0.0343695 | 0.0014383 | ENSG00000108799 | EZH1 | retained_intron | 0.8162796 |
| DRIMSeq | ENST00000469631 | 0.0416977 | 0.0000000 | 0.0015088 | ENSG00000106462 | EZH2 | retained_intron | 1.4374563 |
| DRIMSeq | ENST00000483012 | 0.0416977 | 0.0000000 | 0.0015088 | ENSG00000106462 | EZH2 | nonsense_mediated_decay | -1.4374563 |
| DRIMSeq | ENST00000494172 | 0.0162533 | 0.0034118 | 0.0001428 | ENSG00000168754 | FAM178B | retained_intron | 1.8175405 |
| DRIMSeq | ENST00000520074 | 0.0162533 | 0.0499345 | 0.0020896 | ENSG00000168754 | FAM178B | processed_transcript | -1.3328915 |
| DRIMSeq | ENST00000491999 | 0.0272974 | 0.0061334 | 0.0002567 | ENSG00000172366 | FAM195A | nonsense_mediated_decay | -0.9111268 |
| DRIMSeq | ENST00000378557 | 0.0078481 | 0.0005022 | 0.0000070 | ENSG00000005238 | FAM214B | protein_coding | 3.4570075 |
| DRIMSeq | ENST00000548869 | 0.0384582 | 0.0212725 | 0.0004451 | ENSG00000204856 | FAM216A | retained_intron | 1.3419722 |
| DRIMSeq | ENST00000252530 | 0.0120253 | 0.0019652 | 0.0000274 | ENSG00000130244 | FAM98C | protein_coding | -1.2970493 |
| DRIMSeq | ENST00000467237 | 0.0398035 | 0.0425969 | 0.0008913 | ENSG00000164896 | FASTK | retained_intron | 0.9241629 |
| DRIMSeq | ENST00000289902 | 0.0169973 | 0.0019032 | 0.0000796 | ENSG00000158869 | FCER1G | protein_coding | -1.5696622 |
| DRIMSeq | ENST00000595713 | 0.0271797 | 0.0000000 | 0.0006749 | ENSG00000090920 | FCGBP | processed_transcript | 1.5920778 |
| DRIMSeq | ENST00000221347 | 0.0271797 | 0.0000000 | 0.0006749 | ENSG00000090920 | FCGBP | protein_coding | -1.5920778 |
| DRIMSeq | ENST00000345728 | 0.0398035 | 0.0157428 | 0.0001318 | ENSG00000149781 | FERMT3 | protein_coding | -1.4843458 |
| DRIMSeq | ENST00000586042 | 0.0195353 | 0.0019929 | 0.0000834 | ENSG00000070388 | FGF22 | protein_coding | -1.8427072 |
| DRIMSeq | ENST00000380991 | 0.0463093 | 0.0000000 | 0.0017997 | ENSG00000119782 | FKBP1B | protein_coding | 0.9043200 |
| DRIMSeq | ENST00000380986 | 0.0463093 | 0.0000000 | 0.0017997 | ENSG00000119782 | FKBP1B | protein_coding | -0.9043200 |
| DRIMSeq | ENST00000463443 | 0.0039202 | 0.0224129 | 0.0003126 | ENSG00000122642 | FKBP9 | processed_transcript | 1.1281675 |
| DRIMSeq | ENST00000330753 | 0.0098454 | 0.0001919 | 0.0000040 | ENSG00000185070 | FLRT2 | protein_coding | -0.7734551 |
| DRIMSeq | ENST00000570759 | 0.0138555 | 0.0005093 | 0.0000107 | ENSG00000059122 | FLYWCH1 | processed_transcript | 0.8153756 |
| DRIMSeq | ENST00000263578 | 0.0068715 | 0.0003491 | 0.0000073 | ENSG00000110074 | FOXRED1 | protein_coding | -1.1161403 |
| DRIMSeq | ENST00000479318 | 0.0000133 | 0.0000069 | 0.0000001 | ENSG00000149531 | FRG1B | nonsense_mediated_decay | 1.1325671 |
| DRIMSeq | ENST00000358464 | 0.0000133 | 0.0120715 | 0.0001684 | ENSG00000149531 | FRG1B | protein_coding | -0.7919398 |
| DRIMSeq | ENST00000439954 | 0.0000133 | 0.0365632 | 0.0005100 | ENSG00000149531 | FRG1B | protein_coding | -0.7661920 |
| DRIMSeq | ENST00000491130 | 0.0398035 | 0.0000000 | 0.0013437 | ENSG00000170324 | FRMPD2 | retained_intron | -2.9726224 |
| DRIMSeq | ENST00000486151 | 0.0398035 | 0.0000000 | 0.0013437 | ENSG00000170324 | FRMPD2 | retained_intron | 2.9726224 |
| DRIMSeq | ENST00000480823 | 0.0276992 | 0.0041309 | 0.0000864 | ENSG00000163430 | FSTL1 | protein_coding | -1.4761821 |
| DRIMSeq | ENST00000472006 | 0.0242750 | 0.0155143 | 0.0006492 | ENSG00000107164 | FUBP3 | processed_transcript | 0.9753220 |
| DRIMSeq | ENST00000349752 | 0.0471741 | 0.0389492 | 0.0005433 | ENSG00000158089 | GALNT14 | protein_coding | -1.3891135 |
| DRIMSeq | ENST00000389266 | 0.0287317 | 0.0000000 | 0.0007504 | ENSG00000106105 | GARS | protein_coding | -0.9835145 |
| DRIMSeq | ENST00000496643 | 0.0287317 | 0.0000000 | 0.0007504 | ENSG00000106105 | GARS | retained_intron | 0.9835145 |
| DRIMSeq | ENST00000268699 | 0.0458349 | 0.0219996 | 0.0004603 | ENSG00000141013 | GAS8 | protein_coding | -0.9257144 |
| DRIMSeq | ENST00000445230 | 0.0108017 | 0.0012498 | 0.0000523 | ENSG00000239521 | GATS | processed_transcript | 0.9204799 |
| DRIMSeq | ENST00000543273 | 0.0108017 | 0.0350759 | 0.0014678 | ENSG00000239521 | GATS | processed_transcript | -0.7630822 |
| DRIMSeq | ENST00000551549 | 0.0272974 | 0.0031164 | 0.0001304 | ENSG00000089154 | GCN1L1 | retained_intron | 0.7496507 |
| DRIMSeq | ENST00000591809 | 0.0498511 | 0.0096053 | 0.0004020 | ENSG00000179168 | GGN | processed_transcript | 1.6490569 |
| DRIMSeq | ENST00000487388 | 0.0328170 | 0.0000000 | 0.0009498 | ENSG00000106560 | GIMAP2 | retained_intron | 1.0594073 |
| DRIMSeq | ENST00000223293 | 0.0328170 | 0.0000000 | 0.0009498 | ENSG00000106560 | GIMAP2 | protein_coding | -1.0594073 |
| DRIMSeq | ENST00000413616 | 0.0263282 | 0.0000000 | 0.0006414 | ENSG00000229894 | GK3P | processed_pseudogene | -1.7180500 |
| DRIMSeq | ENST00000505354 | 0.0263282 | 0.0000000 | 0.0006414 | ENSG00000229894 | GK3P | processed_pseudogene | 1.7180500 |
| DRIMSeq | ENST00000377960 | 0.0095436 | 0.0008566 | 0.0000358 | ENSG00000122694 | GLIPR2 | protein_coding | -1.8208326 |
| DRIMSeq | ENST00000450791 | 0.0427593 | 0.0099006 | 0.0002072 | ENSG00000090615 | GOLGA3 | protein_coding | -0.6336461 |
| DRIMSeq | ENST00000264039 | 0.0221559 | 0.0000000 | 0.0004593 | ENSG00000063660 | GPC1 | protein_coding | -0.6498567 |
| DRIMSeq | ENST00000426280 | 0.0221559 | 0.0000000 | 0.0004593 | ENSG00000063660 | GPC1 | protein_coding | 0.6498567 |
| DRIMSeq | ENST00000397088 | 0.0456265 | 0.0039597 | 0.0000829 | ENSG00000164850 | GPER1 | protein_coding | -1.1971096 |
| DRIMSeq | ENST00000264126 | 0.0114729 | 0.0013986 | 0.0000293 | ENSG00000121957 | GPSM2 | protein_coding | -1.0249464 |
| DRIMSeq | ENST00000262895 | 0.0390499 | 0.0129424 | 0.0005416 | ENSG00000105737 | GRIK5 | protein_coding | -0.9642173 |
| DRIMSeq | ENST00000370963 | 0.0440348 | 0.0279542 | 0.0011698 | ENSG00000170899 | GSTA4 | protein_coding | -0.8130303 |
| DRIMSeq | ENST00000394730 | 0.0215993 | 0.0217317 | 0.0004547 | ENSG00000138780 | GSTCD | protein_coding | 1.9446981 |
| DRIMSeq | ENST00000515279 | 0.0215993 | 0.0280728 | 0.0005874 | ENSG00000138780 | GSTCD | protein_coding | -1.0478814 |
| DRIMSeq | ENST00000358406 | 0.0074888 | 0.0097645 | 0.0001362 | ENSG00000197448 | GSTK1 | protein_coding | -0.5488367 |
| DRIMSeq | ENST00000262903 | 0.0120253 | 0.0002114 | 0.0000029 | ENSG00000085382 | HACE1 | protein_coding | -1.1461413 |
| DRIMSeq | ENST00000206474 | 0.0232151 | 0.0276067 | 0.0001925 | ENSG00000092036 | HAUS4 | protein_coding | -2.2367704 |
| DRIMSeq | ENST00000498366 | 0.0232151 | 0.0124280 | 0.0002600 | ENSG00000100429 | HDAC10 | processed_transcript | -1.8389932 |
| DRIMSeq | ENST00000305264 | 0.0010624 | 0.0000064 | 0.0000001 | ENSG00000171720 | HDAC3 | protein_coding | -1.3820177 |
| DRIMSeq | ENST00000504994 | 0.0329283 | 0.0048199 | 0.0002017 | ENSG00000138641 | HERC3 | processed_transcript | 0.9366559 |
| DRIMSeq | ENST00000506842 | 0.0025089 | 0.0002613 | 0.0000055 | ENSG00000138642 | HERC6 | retained_intron | 1.1438326 |
| DRIMSeq | ENST00000264346 | 0.0025089 | 0.0007131 | 0.0000149 | ENSG00000138642 | HERC6 | protein_coding | -0.8447323 |
| DRIMSeq | ENST00000414928 | 0.0159208 | 0.0020979 | 0.0000878 | ENSG00000198130 | HIBCH | nonsense_mediated_decay | 1.5829753 |
| DRIMSeq | ENST00000377777 | 0.0220696 | 0.0000000 | 0.0004522 | ENSG00000158373 | HIST1H2BD | protein_coding | -0.9484472 |
| DRIMSeq | ENST00000289316 | 0.0220696 | 0.0000000 | 0.0004522 | ENSG00000158373 | HIST1H2BD | protein_coding | 0.9484472 |
| DRIMSeq | ENST00000278715 | 0.0302169 | 0.0146899 | 0.0006147 | ENSG00000256269 | HMBS | protein_coding | -2.2032844 |
| DRIMSeq | ENST00000374490 | 0.0036200 | 0.0001174 | 0.0000016 | ENSG00000117305 | HMGCL | protein_coding | -1.1073140 |
| DRIMSeq | ENST00000450735 | 0.0151744 | 0.0182778 | 0.0002550 | ENSG00000103942 | HOMER2 | protein_coding | -0.6645634 |
| DRIMSeq | ENST00000312239 | 0.0000716 | 0.0044433 | 0.0000620 | ENSG00000127483 | HP1BP3 | protein_coding | -0.7854513 |
| DRIMSeq | ENST00000508413 | 0.0007032 | 0.0000171 | 0.0000007 | ENSG00000198189 | HSD17B11 | processed_transcript | 1.8819957 |
| DRIMSeq | ENST00000358290 | 0.0007032 | 0.0023451 | 0.0000981 | ENSG00000198189 | HSD17B11 | protein_coding | -1.0319406 |
| DRIMSeq | ENST00000554643 | 0.0250609 | 0.0409762 | 0.0008574 | ENSG00000025423 | HSD17B6 | protein_coding | 1.7116236 |
| DRIMSeq | ENST00000380405 | 0.0014299 | 0.0001807 | 0.0000076 | ENSG00000120694 | HSPH1 | protein_coding | 1.9972896 |
| DRIMSeq | ENST00000320027 | 0.0014299 | 0.0002259 | 0.0000095 | ENSG00000120694 | HSPH1 | protein_coding | -1.5100934 |
| DRIMSeq | ENST00000438323 | 0.0098938 | 0.0024063 | 0.0000503 | ENSG00000068079 | IFI35 | protein_coding | -1.8035612 |
| DRIMSeq | ENST00000549628 | 0.0249355 | 0.0015050 | 0.0000315 | ENSG00000167779 | IGFBP6 | processed_transcript | 2.2795989 |
| DRIMSeq | ENST00000519735 | 0.0313144 | 0.0127904 | 0.0005352 | ENSG00000104365 | IKBKB | protein_coding | -0.8395687 |
| DRIMSeq | ENST00000589173 | 0.0114150 | 0.0054709 | 0.0002289 | ENSG00000129351 | ILF3 | retained_intron | 0.7791584 |
| DRIMSeq | ENST00000256108 | 0.0169973 | 0.0000000 | 0.0002969 | ENSG00000133731 | IMPA1 | protein_coding | -1.0263682 |
| DRIMSeq | ENST00000522997 | 0.0169973 | 0.0000000 | 0.0002969 | ENSG00000133731 | IMPA1 | protein_coding | 1.0263682 |
| DRIMSeq | ENST00000326739 | 0.0241927 | 0.0032665 | 0.0001367 | ENSG00000178035 | IMPDH2 | protein_coding | -0.8081971 |
| DRIMSeq | ENST00000243786 | 0.0397215 | 0.0000000 | 0.0013212 | ENSG00000123999 | INHA | protein_coding | -1.6758153 |
| DRIMSeq | ENST00000489456 | 0.0397215 | 0.0000000 | 0.0013212 | ENSG00000123999 | INHA | processed_transcript | 1.6758153 |
| DRIMSeq | ENST00000498104 | 0.0388082 | 0.0319763 | 0.0006691 | ENSG00000173226 | IQCB1 | protein_coding | 1.0429110 |
| DRIMSeq | ENST00000228799 | 0.0281745 | 0.0000000 | 0.0007199 | ENSG00000111203 | ITFG2 | protein_coding | -1.0595920 |
| DRIMSeq | ENST00000552005 | 0.0281745 | 0.0000000 | 0.0007199 | ENSG00000111203 | ITFG2 | processed_transcript | 1.0595920 |
| DRIMSeq | ENST00000356798 | 0.0416977 | 0.0000000 | 0.0015095 | ENSG00000005844 | ITGAL | protein_coding | -1.4890878 |
| DRIMSeq | ENST00000562020 | 0.0416977 | 0.0000000 | 0.0015095 | ENSG00000005844 | ITGAL | retained_intron | 1.4890878 |
| DRIMSeq | ENST00000397146 | 0.0036630 | 0.0442328 | 0.0006170 | ENSG00000123243 | ITIH5 | protein_coding | -1.6642891 |
| DRIMSeq | ENST00000366758 | 0.0415266 | 0.0076802 | 0.0003214 | ENSG00000081692 | JMJD4 | protein_coding | -1.5606634 |
| DRIMSeq | ENST00000397299 | 0.0181827 | 0.0014837 | 0.0000621 | ENSG00000243789 | JMJD7 | protein_coding | -1.2706256 |
| DRIMSeq | ENST00000240662 | 0.0398035 | 0.0000000 | 0.0013400 | ENSG00000121361 | KCNJ8 | protein_coding | -1.9991853 |
| DRIMSeq | ENST00000537950 | 0.0398035 | 0.0000000 | 0.0013400 | ENSG00000121361 | KCNJ8 | protein_coding | 1.9991853 |
| DRIMSeq | ENST00000472869 | 0.0139758 | 0.0018995 | 0.0000795 | ENSG00000135750 | KCNK1 | processed_transcript | 1.0871946 |
| DRIMSeq | ENST00000357249 | 0.0192964 | 0.0000000 | 0.0003582 | ENSG00000075043 | KCNQ2 | protein_coding | -0.9664944 |
| DRIMSeq | ENST00000482957 | 0.0192964 | 0.0000000 | 0.0003582 | ENSG00000075043 | KCNQ2 | processed_transcript | 0.9664944 |
| DRIMSeq | ENST00000298480 | 0.0215033 | 0.0008593 | 0.0000120 | ENSG00000107147 | KCNT1 | protein_coding | -1.2598015 |
| DRIMSeq | ENST00000470573 | 0.0169973 | 0.0009326 | 0.0000195 | ENSG00000117139 | KDM5B | processed_transcript | 0.9920578 |
| DRIMSeq | ENST00000484801 | 0.0494148 | 0.0117981 | 0.0004937 | ENSG00000135314 | KHDC1 | processed_transcript | 0.8777868 |
| DRIMSeq | ENST00000327300 | 0.0206276 | 0.0000000 | 0.0003973 | ENSG00000121774 | KHDRBS1 | protein_coding | -0.8538406 |
| DRIMSeq | ENST00000484270 | 0.0206276 | 0.0000000 | 0.0003973 | ENSG00000121774 | KHDRBS1 | processed_transcript | 0.8538406 |
| DRIMSeq | ENST00000425103 | 0.0463093 | 0.0070284 | 0.0002941 | ENSG00000170871 | KIAA0232 | protein_coding | -0.8978934 |
| DRIMSeq | ENST00000443149 | 0.0058570 | 0.0212210 | 0.0002960 | ENSG00000183354 | KIAA2026 | processed_transcript | 0.9813160 |
| DRIMSeq | ENST00000534023 | 0.0002283 | 0.0000173 | 0.0000004 | ENSG00000174996 | KLC2 | retained_intron | 1.5564606 |
| DRIMSeq | ENST00000347162 | 0.0120253 | 0.0000000 | 0.0001537 | ENSG00000137171 | KLC4 | protein_coding | -1.0187363 |
| DRIMSeq | ENST00000463168 | 0.0120253 | 0.0000000 | 0.0001537 | ENSG00000137171 | KLC4 | retained_intron | 1.0187363 |
| DRIMSeq | ENST00000554589 | 0.0319243 | 0.0054493 | 0.0001140 | ENSG00000165516 | KLHDC2 | protein_coding | -1.3062247 |
| DRIMSeq | ENST00000328879 | 0.0237692 | 0.0014938 | 0.0000313 | ENSG00000099910 | KLHL22 | protein_coding | -0.7030909 |
| DRIMSeq | ENST00000392647 | 0.0178093 | 0.0000000 | 0.0003152 | ENSG00000213160 | KLHL23 | protein_coding | 1.1899031 |
| DRIMSeq | ENST00000437875 | 0.0178093 | 0.0000000 | 0.0003152 | ENSG00000213160 | KLHL23 | protein_coding | -1.1899031 |
| DRIMSeq | ENST00000344442 | 0.0398035 | 0.0000000 | 0.0013394 | ENSG00000174720 | LARP7 | protein_coding | 0.8310427 |
| DRIMSeq | ENST00000324052 | 0.0398035 | 0.0000000 | 0.0013394 | ENSG00000174720 | LARP7 | protein_coding | -0.8310427 |
| DRIMSeq | ENST00000334869 | 0.0154020 | 0.0012476 | 0.0000522 | ENSG00000100600 | LGMN | protein_coding | -1.1501401 |
| DRIMSeq | ENST00000396595 | 0.0313642 | 0.0082521 | 0.0003453 | ENSG00000064042 | LIMCH1 | protein_coding | -0.8440741 |
| DRIMSeq | ENST00000221459 | 0.0078481 | 0.0000000 | 0.0000716 | ENSG00000104863 | LIN7B | protein_coding | -1.4942078 |
| DRIMSeq | ENST00000474252 | 0.0078481 | 0.0000000 | 0.0000716 | ENSG00000104863 | LIN7B | retained_intron | 1.4942078 |
| DRIMSeq | ENST00000510736 | 0.0168681 | 0.0058883 | 0.0001232 | ENSG00000251372 | LINC00499 | lincRNA | -1.1402876 |
| DRIMSeq | ENST00000502757 | 0.0168681 | 0.0093774 | 0.0001962 | ENSG00000251372 | LINC00499 | lincRNA | 0.9281199 |
| DRIMSeq | ENST00000555246 | 0.0452514 | 0.0000000 | 0.0016871 | ENSG00000258700 | LINC00871 | lincRNA | -1.1031793 |
| DRIMSeq | ENST00000556886 | 0.0452514 | 0.0000000 | 0.0016871 | ENSG00000258700 | LINC00871 | lincRNA | 1.1031793 |
| DRIMSeq | ENST00000429464 | 0.0133295 | 0.0011088 | 0.0000464 | ENSG00000235597 | LINC01102 | lincRNA | 1.1393503 |
| DRIMSeq | ENST00000449448 | 0.0125518 | 0.0099299 | 0.0001039 | ENSG00000233723 | LINC01122 | lincRNA | -2.8839416 |
| DRIMSeq | ENST00000262301 | 0.0187088 | 0.0026834 | 0.0000561 | ENSG00000103227 | LMF1 | protein_coding | -1.0928551 |
| DRIMSeq | ENST00000345941 | 0.0240234 | 0.0041130 | 0.0000574 | ENSG00000139679 | LPAR6 | protein_coding | -1.5231058 |
| DRIMSeq | ENST00000336356 | 0.0389363 | 0.0000000 | 0.0012619 | ENSG00000121207 | LRAT | protein_coding | -2.6677087 |
| DRIMSeq | ENST00000510733 | 0.0389363 | 0.0000000 | 0.0012619 | ENSG00000121207 | LRAT | retained_intron | 2.6677087 |
| DRIMSeq | ENST00000558799 | 0.0187451 | 0.0000000 | 0.0003436 | ENSG00000137821 | LRRC49 | processed_transcript | 1.1908249 |
| DRIMSeq | ENST00000260382 | 0.0187451 | 0.0000000 | 0.0003436 | ENSG00000137821 | LRRC49 | protein_coding | -1.1908249 |
| DRIMSeq | ENST00000397130 | 0.0169822 | 0.0018764 | 0.0000785 | ENSG00000180979 | LRRC57 | protein_coding | -1.1503256 |
| DRIMSeq | ENST00000323443 | 0.0169822 | 0.0106776 | 0.0004468 | ENSG00000180979 | LRRC57 | protein_coding | 1.2068703 |
| DRIMSeq | ENST00000440313 | 0.0471573 | 0.0054566 | 0.0000761 | ENSG00000184154 | LRTOMT | protein_coding | 1.4097454 |
| DRIMSeq | ENST00000396052 | 0.0406755 | 0.0040264 | 0.0000842 | ENSG00000102897 | LYRM1 | protein_coding | 0.9813317 |
| DRIMSeq | ENST00000478551 | 0.0241927 | 0.0030862 | 0.0001291 | ENSG00000163818 | LZTFL1 | retained_intron | 1.0888532 |
| DRIMSeq | ENST00000507385 | 0.0000716 | 0.0000003 | 0.0000000 | ENSG00000161021 | MAML1 | retained_intron | 2.1148540 |
| DRIMSeq | ENST00000292599 | 0.0000716 | 0.0254642 | 0.0005328 | ENSG00000161021 | MAML1 | protein_coding | -0.9514561 |
| DRIMSeq | ENST00000285599 | 0.0440348 | 0.0000000 | 0.0016202 | ENSG00000013288 | MAN2B2 | protein_coding | -0.8782643 |
| DRIMSeq | ENST00000505907 | 0.0440348 | 0.0000000 | 0.0016202 | ENSG00000013288 | MAN2B2 | protein_coding | 0.8782643 |
| DRIMSeq | ENST00000358935 | 0.0232151 | 0.0086004 | 0.0003599 | ENSG00000198060 | MARCH5 | protein_coding | -0.6771257 |
| DRIMSeq | ENST00000262027 | 0.0115249 | 0.0000000 | 0.0001416 | ENSG00000166986 | MARS | protein_coding | -1.0842761 |
| DRIMSeq | ENST00000548202 | 0.0115249 | 0.0000000 | 0.0001416 | ENSG00000166986 | MARS | retained_intron | 1.0842761 |
| DRIMSeq | ENST00000251472 | 0.0241681 | 0.0030528 | 0.0001278 | ENSG00000105613 | MAST1 | protein_coding | -0.7833693 |
| DRIMSeq | ENST00000310132 | 0.0407671 | 0.0259631 | 0.0005432 | ENSG00000007264 | MATK | protein_coding | 1.4769804 |
| DRIMSeq | ENST00000457839 | 0.0098454 | 0.0016106 | 0.0000674 | ENSG00000141644 | MBD1 | protein_coding | -0.8487705 |
| DRIMSeq | ENST00000586884 | 0.0098454 | 0.0241358 | 0.0010100 | ENSG00000141644 | MBD1 | retained_intron | 0.6725778 |
| DRIMSeq | ENST00000397865 | 0.0359426 | 0.0082221 | 0.0003441 | ENSG00000197971 | MBP | protein_coding | 0.9356743 |
| DRIMSeq | ENST00000263702 | 0.0099097 | 0.0006252 | 0.0000262 | ENSG00000116353 | MECR | protein_coding | -1.2668671 |
| DRIMSeq | ENST00000564661 | 0.0151134 | 0.0414936 | 0.0008682 | ENSG00000103260 | METRN | retained_intron | 0.8569623 |
| DRIMSeq | ENST00000301327 | 0.0207421 | 0.0025670 | 0.0001074 | ENSG00000167700 | MFSD3 | protein_coding | -0.9814941 |
| DRIMSeq | ENST00000296468 | 0.0248575 | 0.0000000 | 0.0005845 | ENSG00000164073 | MFSD8 | protein_coding | -1.0212083 |
| DRIMSeq | ENST00000503928 | 0.0248575 | 0.0000000 | 0.0005845 | ENSG00000164073 | MFSD8 | processed_transcript | 1.0212083 |
| DRIMSeq | ENST00000496253 | 0.0021572 | 0.0000275 | 0.0000011 | ENSG00000135953 | MFSD9 | processed_transcript | -3.6828703 |
| DRIMSeq | ENST00000333055 | 0.0386784 | 0.0046563 | 0.0000974 | ENSG00000131446 | MGAT1 | protein_coding | -1.0753636 |
| DRIMSeq | ENST00000341184 | 0.0248575 | 0.0026858 | 0.0001124 | ENSG00000128268 | MGAT3 | protein_coding | -0.7326571 |
| DRIMSeq | ENST00000597600 | 0.0445188 | 0.0000000 | 0.0016564 | ENSG00000261857 | MIA | protein_coding | -2.0785851 |
| DRIMSeq | ENST00000593317 | 0.0445188 | 0.0000000 | 0.0016564 | ENSG00000261857 | MIA | retained_intron | 2.0785851 |
| DRIMSeq | ENST00000290130 | 0.0250609 | 0.0000000 | 0.0005989 | ENSG00000159055 | MIS18A | protein_coding | -1.4702847 |
| DRIMSeq | ENST00000486363 | 0.0250609 | 0.0000000 | 0.0005989 | ENSG00000159055 | MIS18A | processed_transcript | 1.4702847 |
| DRIMSeq | ENST00000355630 | 0.0398035 | 0.0182712 | 0.0007646 | ENSG00000196588 | MKL1 | protein_coding | -0.6947315 |
| DRIMSeq | ENST00000591601 | 0.0001876 | 0.0000318 | 0.0000007 | ENSG00000099875 | MKNK2 | protein_coding | -1.3362476 |
| DRIMSeq | ENST00000309340 | 0.0001876 | 0.0001463 | 0.0000031 | ENSG00000099875 | MKNK2 | protein_coding | 1.4461172 |
| DRIMSeq | ENST00000566203 | 0.0386784 | 0.0063844 | 0.0002672 | ENSG00000126005 | MMP24-AS1 | antisense | 0.9106349 |
| DRIMSeq | ENST00000483013 | 0.0150745 | 0.0025381 | 0.0000354 | ENSG00000204655 | MOG | protein_coding | 2.1036125 |
| DRIMSeq | ENST00000376917 | 0.0150745 | 0.0407875 | 0.0005689 | ENSG00000204655 | MOG | protein_coding | -0.9537144 |
| DRIMSeq | ENST00000569021 | 0.0076054 | 0.0000000 | 0.0000653 | ENSG00000135698 | MPHOSPH6 | protein_coding | 0.9421147 |
| DRIMSeq | ENST00000258169 | 0.0076054 | 0.0000000 | 0.0000653 | ENSG00000135698 | MPHOSPH6 | protein_coding | -0.9421147 |
| DRIMSeq | ENST00000435114 | 0.0138555 | 0.0130005 | 0.0001813 | ENSG00000115204 | MPV17 | protein_coding | 1.8105675 |
| DRIMSeq | ENST00000380044 | 0.0138555 | 0.0164623 | 0.0002296 | ENSG00000115204 | MPV17 | protein_coding | -0.9580214 |
| DRIMSeq | ENST00000479638 | 0.0471741 | 0.0000000 | 0.0018864 | ENSG00000112110 | MRPL18 | processed_transcript | 0.8030617 |
| DRIMSeq | ENST00000367034 | 0.0471741 | 0.0000000 | 0.0018864 | ENSG00000112110 | MRPL18 | protein_coding | -0.8030617 |
| DRIMSeq | ENST00000418740 | 0.0459801 | 0.0000000 | 0.0017712 | ENSG00000062582 | MRPS24 | nonsense_mediated_decay | 0.6589720 |
| DRIMSeq | ENST00000317534 | 0.0459801 | 0.0000000 | 0.0017712 | ENSG00000062582 | MRPS24 | protein_coding | -0.6589720 |
| DRIMSeq | ENST00000609421 | 0.0388082 | 0.0068598 | 0.0002871 | ENSG00000173171 | MTX1 | protein_coding | -0.7560438 |
| DRIMSeq | ENST00000594784 | 0.0071631 | 0.0002766 | 0.0000039 | ENSG00000141971 | MVB12A | protein_coding | -2.6686215 |
| DRIMSeq | ENST00000398598 | 0.0097751 | 0.0004273 | 0.0000179 | ENSG00000157601 | MX1 | protein_coding | -0.9772560 |
| DRIMSeq | ENST00000484465 | 0.0097751 | 0.0072356 | 0.0003028 | ENSG00000157601 | MX1 | retained_intron | 0.8147220 |
| DRIMSeq | ENST00000409745 | 0.0142257 | 0.0000000 | 0.0002049 | ENSG00000185105 | MYADML2 | protein_coding | 2.4962177 |
| DRIMSeq | ENST00000330655 | 0.0142257 | 0.0000000 | 0.0002049 | ENSG00000185105 | MYADML2 | protein_coding | -2.4962177 |
| DRIMSeq | ENST00000303775 | 0.0212294 | 0.0069504 | 0.0002909 | ENSG00000156239 | N6AMT1 | protein_coding | -1.0417695 |
| DRIMSeq | ENST00000351429 | 0.0212294 | 0.0090333 | 0.0003780 | ENSG00000156239 | N6AMT1 | protein_coding | 1.1017655 |
| DRIMSeq | ENST00000342556 | 0.0104651 | 0.0011302 | 0.0000473 | ENSG00000166886 | NAB2 | protein_coding | 1.7373494 |
| DRIMSeq | ENST00000300131 | 0.0104651 | 0.0157505 | 0.0006591 | ENSG00000166886 | NAB2 | protein_coding | -1.3735670 |
| DRIMSeq | ENST00000341463 | 0.0456265 | 0.0085045 | 0.0003559 | ENSG00000139579 | NABP2 | protein_coding | -1.2160974 |
| DRIMSeq | ENST00000310701 | 0.0115249 | 0.0000000 | 0.0001417 | ENSG00000122497 | NBPF14 | protein_coding | 2.4292292 |
| DRIMSeq | ENST00000369219 | 0.0115249 | 0.0000000 | 0.0001417 | ENSG00000122497 | NBPF14 | protein_coding | -2.4292292 |
| DRIMSeq | ENST00000315579 | 0.0415266 | 0.0075328 | 0.0003152 | ENSG00000010292 | NCAPD2 | protein_coding | -1.1149720 |
| DRIMSeq | ENST00000420993 | 0.0050465 | 0.0002598 | 0.0000109 | ENSG00000025770 | NCAPH2 | protein_coding | -0.8220696 |
| DRIMSeq | ENST00000517331 | 0.0036062 | 0.0002331 | 0.0000098 | ENSG00000104419 | NDRG1 | processed_transcript | 1.4785722 |
| DRIMSeq | ENST00000323851 | 0.0036062 | 0.0410208 | 0.0017166 | ENSG00000104419 | NDRG1 | protein_coding | -0.6970293 |
| DRIMSeq | ENST00000268668 | 0.0381589 | 0.0000000 | 0.0011838 | ENSG00000140990 | NDUFB10 | protein_coding | -1.1272128 |
| DRIMSeq | ENST00000543683 | 0.0381589 | 0.0000000 | 0.0011838 | ENSG00000140990 | NDUFB10 | protein_coding | 1.1272128 |
| DRIMSeq | ENST00000392179 | 0.0066668 | 0.0012946 | 0.0000542 | ENSG00000158864 | NDUFS2 | protein_coding | 1.9491806 |
| DRIMSeq | ENST00000367993 | 0.0066668 | 0.0107253 | 0.0004488 | ENSG00000158864 | NDUFS2 | protein_coding | -1.1117745 |
| DRIMSeq | ENST00000375238 | 0.0150533 | 0.0016661 | 0.0000697 | ENSG00000125967 | NECAB3 | protein_coding | -1.2736157 |
| DRIMSeq | ENST00000436750 | 0.0078481 | 0.0000000 | 0.0000723 | ENSG00000154328 | NEIL2 | protein_coding | -0.9758516 |
| DRIMSeq | ENST00000284503 | 0.0078481 | 0.0000000 | 0.0000723 | ENSG00000154328 | NEIL2 | protein_coding | 0.9758516 |
| DRIMSeq | ENST00000233027 | 0.0475025 | 0.0294047 | 0.0012305 | ENSG00000114904 | NEK4 | protein_coding | -0.6494533 |
| DRIMSeq | ENST00000493199 | 0.0475025 | 0.0304847 | 0.0012757 | ENSG00000114904 | NEK4 | retained_intron | 0.6949319 |
| DRIMSeq | ENST00000404295 | 0.0312475 | 0.0035977 | 0.0000376 | ENSG00000153406 | NMRAL1 | protein_coding | -1.4254810 |
| DRIMSeq | ENST00000378165 | 0.0236176 | 0.0329240 | 0.0004593 | ENSG00000152465 | NMT2 | protein_coding | -0.5872966 |
| DRIMSeq | ENST00000496938 | 0.0236176 | 0.0024103 | 0.0000504 | ENSG00000188976 | NOC2L | processed_transcript | 1.7773365 |
| DRIMSeq | ENST00000362074 | 0.0077076 | 0.0067696 | 0.0001416 | ENSG00000213240 | NOTCH2NL | protein_coding | -1.3892162 |
| DRIMSeq | ENST00000468544 | 0.0232446 | 0.0060152 | 0.0002517 | ENSG00000107833 | NPM3 | processed_transcript | 2.9644529 |
| DRIMSeq | ENST00000425241 | 0.0115824 | 0.0013028 | 0.0000273 | ENSG00000177463 | NR2C2 | protein_coding | -0.9012020 |
| DRIMSeq | ENST00000352171 | 0.0215033 | 0.0000000 | 0.0004259 | ENSG00000078618 | NRD1 | protein_coding | -0.7807143 |
| DRIMSeq | ENST00000464385 | 0.0215033 | 0.0000000 | 0.0004259 | ENSG00000078618 | NRD1 | processed_transcript | 0.7807143 |
| DRIMSeq | ENST00000287437 | 0.0194115 | 0.0023848 | 0.0000499 | ENSG00000156831 | NSMCE2 | protein_coding | -1.0658239 |
| DRIMSeq | ENST00000252594 | 0.0005851 | 0.0003100 | 0.0000130 | ENSG00000130305 | NSUN5 | protein_coding | 2.1673125 |
| DRIMSeq | ENST00000438747 | 0.0005851 | 0.0003351 | 0.0000140 | ENSG00000130305 | NSUN5 | protein_coding | -1.6241298 |
| DRIMSeq | ENST00000562263 | 0.0196447 | 0.0138178 | 0.0005782 | ENSG00000095906 | NUBP2 | protein_coding | 1.7718911 |
| DRIMSeq | ENST00000279206 | 0.0496424 | 0.0140339 | 0.0001958 | ENSG00000149761 | NUDT22 | protein_coding | -0.7796945 |
| DRIMSeq | ENST00000552283 | 0.0249355 | 0.0000000 | 0.0005907 | ENSG00000075188 | NUP37 | protein_coding | -0.9763259 |
| DRIMSeq | ENST00000550459 | 0.0249355 | 0.0000000 | 0.0005907 | ENSG00000075188 | NUP37 | protein_coding | 0.9763259 |
| DRIMSeq | ENST00000462534 | 0.0114150 | 0.0270758 | 0.0005665 | ENSG00000124006 | OBSL1 | retained_intron | 0.8496862 |
| DRIMSeq | ENST00000374103 | 0.0414476 | 0.0000000 | 0.0014587 | ENSG00000197444 | OGDHL | protein_coding | -0.8005873 |
| DRIMSeq | ENST00000496884 | 0.0414476 | 0.0000000 | 0.0014587 | ENSG00000197444 | OGDHL | processed_transcript | 0.8005873 |
| DRIMSeq | ENST00000358603 | 0.0212161 | 0.0027399 | 0.0000573 | ENSG00000162600 | OMA1 | protein_coding | -2.0197874 |
| DRIMSeq | ENST00000338972 | 0.0396600 | 0.0311265 | 0.0013026 | ENSG00000172239 | PAIP1 | protein_coding | 1.1868890 |
| DRIMSeq | ENST00000455170 | 0.0304279 | 0.0162043 | 0.0006781 | ENSG00000238197 | PAXBP1-AS1 | antisense | -1.5482821 |
| DRIMSeq | ENST00000308824 | 0.0115249 | 0.0012746 | 0.0000267 | ENSG00000203880 | PCMTD2 | protein_coding | -0.7153863 |
| DRIMSeq | ENST00000355703 | 0.0359426 | 0.0000000 | 0.0010827 | ENSG00000197136 | PCNXL3 | protein_coding | -2.3042521 |
| DRIMSeq | ENST00000531045 | 0.0359426 | 0.0000000 | 0.0010827 | ENSG00000197136 | PCNXL3 | processed_transcript | 2.3042521 |
| DRIMSeq | ENST00000490749 | 0.0238427 | 0.0324560 | 0.0013582 | ENSG00000186642 | PDE2A | retained_intron | 0.8448294 |
| DRIMSeq | ENST00000334456 | 0.0238427 | 0.0350726 | 0.0014677 | ENSG00000186642 | PDE2A | protein_coding | -0.6481895 |
| DRIMSeq | ENST00000261799 | 0.0159637 | 0.0000000 | 0.0002544 | ENSG00000113721 | PDGFRB | protein_coding | -0.9589173 |
| DRIMSeq | ENST00000522466 | 0.0159637 | 0.0000000 | 0.0002544 | ENSG00000113721 | PDGFRB | retained_intron | 0.9589173 |
| DRIMSeq | ENST00000320740 | 0.0020177 | 0.0000887 | 0.0000037 | ENSG00000174516 | PELI3 | protein_coding | -1.4294002 |
| DRIMSeq | ENST00000528752 | 0.0020177 | 0.0431933 | 0.0018075 | ENSG00000174516 | PELI3 | protein_coding | 1.3820407 |
| DRIMSeq | ENST00000381125 | 0.0000060 | 0.0000000 | 0.0000000 | ENSG00000067057 | PFKP | protein_coding | -1.3319847 |
| DRIMSeq | ENST00000413079 | 0.0000060 | 0.0038419 | 0.0000804 | ENSG00000067057 | PFKP | protein_coding | 1.4105881 |
| DRIMSeq | ENST00000381072 | 0.0000060 | 0.0154356 | 0.0003230 | ENSG00000067057 | PFKP | protein_coding | 1.2092338 |
| DRIMSeq | ENST00000373418 | 0.0494148 | 0.0000000 | 0.0020327 | ENSG00000134686 | PHC2 | protein_coding | -0.7791115 |
| DRIMSeq | ENST00000473158 | 0.0494148 | 0.0000000 | 0.0020327 | ENSG00000134686 | PHC2 | processed_transcript | 0.7791115 |
| DRIMSeq | ENST00000263038 | 0.0475025 | 0.0000000 | 0.0019107 | ENSG00000107537 | PHYH | protein_coding | -1.0518197 |
| DRIMSeq | ENST00000396913 | 0.0475025 | 0.0000000 | 0.0019107 | ENSG00000107537 | PHYH | protein_coding | 1.0518197 |
| DRIMSeq | ENST00000356976 | 0.0162533 | 0.0011265 | 0.0000471 | ENSG00000100151 | PICK1 | protein_coding | -0.8216912 |
| DRIMSeq | ENST00000335312 | 0.0348237 | 0.0000000 | 0.0010344 | ENSG00000186111 | PIP5K1C | protein_coding | -0.9284241 |
| DRIMSeq | ENST00000592530 | 0.0348237 | 0.0000000 | 0.0010344 | ENSG00000186111 | PIP5K1C | processed_transcript | 0.9284241 |
| DRIMSeq | ENST00000415826 | 0.0495322 | 0.0174277 | 0.0003646 | ENSG00000176485 | PLA2G16 | protein_coding | -0.7533003 |
| DRIMSeq | ENST00000558505 | 0.0305121 | 0.0013332 | 0.0000139 | ENSG00000137841 | PLCB2 | retained_intron | 2.4198269 |
| DRIMSeq | ENST00000326631 | 0.0036062 | 0.0000432 | 0.0000009 | ENSG00000104886 | PLEKHJ1 | protein_coding | -0.8254397 |
| DRIMSeq | ENST00000246027 | 0.0280838 | 0.0086212 | 0.0003608 | ENSG00000088970 | PLK1S1 | processed_transcript | -0.8372696 |
| DRIMSeq | ENST00000441136 | 0.0280838 | 0.0150369 | 0.0006293 | ENSG00000088970 | PLK1S1 | processed_transcript | 0.9389383 |
| DRIMSeq | ENST00000282903 | 0.0002283 | 0.0000744 | 0.0000016 | ENSG00000152952 | PLOD2 | protein_coding | -1.3183890 |
| DRIMSeq | ENST00000360060 | 0.0002283 | 0.0001135 | 0.0000024 | ENSG00000152952 | PLOD2 | protein_coding | 1.1869520 |
| DRIMSeq | ENST00000383083 | 0.0005305 | 0.0000231 | 0.0000010 | ENSG00000114698 | PLSCR4 | protein_coding | 2.8372644 |
| DRIMSeq | ENST00000354952 | 0.0005305 | 0.0001952 | 0.0000082 | ENSG00000114698 | PLSCR4 | protein_coding | -1.5338732 |
| DRIMSeq | ENST00000368277 | 0.0337064 | 0.0048388 | 0.0002025 | ENSG00000160783 | PMF1 | protein_coding | -0.9042899 |
| DRIMSeq | ENST00000257694 | 0.0495117 | 0.0094672 | 0.0003962 | ENSG00000135241 | PNPLA8 | protein_coding | -0.8264476 |
| DRIMSeq | ENST00000601098 | 0.0080010 | 0.0089282 | 0.0001245 | ENSG00000062822 | POLD1 | protein_coding | -2.1238748 |
| DRIMSeq | ENST00000312419 | 0.0002283 | 0.0000004 | 0.0000000 | ENSG00000175482 | POLD4 | protein_coding | -1.3531897 |
| DRIMSeq | ENST00000441964 | 0.0099020 | 0.0000000 | 0.0001072 | ENSG00000144647 | POMGNT2 | protein_coding | -0.9882633 |
| DRIMSeq | ENST00000344697 | 0.0099020 | 0.0000000 | 0.0001072 | ENSG00000144647 | POMGNT2 | protein_coding | 0.9882633 |
| DRIMSeq | ENST00000455780 | 0.0092235 | 0.0002477 | 0.0000052 | ENSG00000127125 | PPCS | protein_coding | -1.3276938 |
| DRIMSeq | ENST00000263212 | 0.0291518 | 0.0000000 | 0.0007870 | ENSG00000100034 | PPM1F | protein_coding | -1.8458526 |
| DRIMSeq | ENST00000497072 | 0.0291518 | 0.0000000 | 0.0007870 | ENSG00000100034 | PPM1F | processed_transcript | 1.8458526 |
| DRIMSeq | ENST00000587515 | 0.0118089 | 0.0000000 | 0.0001480 | ENSG00000167641 | PPP1R14A | protein_coding | 1.3685234 |
| DRIMSeq | ENST00000301242 | 0.0118089 | 0.0000000 | 0.0001480 | ENSG00000167641 | PPP1R14A | protein_coding | -1.3685234 |
| DRIMSeq | ENST00000433473 | 0.0456265 | 0.0000000 | 0.0017491 | ENSG00000131238 | PPT1 | protein_coding | 1.0647880 |
| DRIMSeq | ENST00000529905 | 0.0456265 | 0.0000000 | 0.0017491 | ENSG00000131238 | PPT1 | nonsense_mediated_decay | -1.0647880 |
| DRIMSeq | ENST00000590895 | 0.0011704 | 0.0005744 | 0.0000120 | ENSG00000122490 | PQLC1 | processed_transcript | 1.1491573 |
| DRIMSeq | ENST00000397778 | 0.0011704 | 0.0300370 | 0.0006285 | ENSG00000122490 | PQLC1 | protein_coding | -0.6299372 |
| DRIMSeq | ENST00000375155 | 0.0314764 | 0.0142295 | 0.0005955 | ENSG00000040487 | PQLC2 | protein_coding | -0.8885630 |
| DRIMSeq | ENST00000547306 | 0.0196835 | 0.0017635 | 0.0000738 | ENSG00000181929 | PRKAG1 | protein_coding | -0.8260371 |
| DRIMSeq | ENST00000547125 | 0.0196835 | 0.0326367 | 0.0013658 | ENSG00000181929 | PRKAG1 | protein_coding | 0.6996628 |
| DRIMSeq | ENST00000592741 | 0.0207287 | 0.0148245 | 0.0002068 | ENSG00000130175 | PRKCSH | protein_coding | -0.7561416 |
| DRIMSeq | ENST00000382622 | 0.0077076 | 0.0015047 | 0.0000630 | ENSG00000111218 | PRMT8 | protein_coding | -1.1724152 |
| DRIMSeq | ENST00000452611 | 0.0077076 | 0.0023268 | 0.0000974 | ENSG00000111218 | PRMT8 | protein_coding | 1.3828282 |
| DRIMSeq | ENST00000334029 | 0.0388082 | 0.0032880 | 0.0000459 | ENSG00000100033 | PRODH | protein_coding | -1.4798192 |
| DRIMSeq | ENST00000337659 | 0.0296621 | 0.0133604 | 0.0002795 | ENSG00000112739 | PRPF4B | protein_coding | -0.8280113 |
| DRIMSeq | ENST00000324684 | 0.0388082 | 0.0021724 | 0.0000227 | ENSG00000161542 | PRPSAP1 | protein_coding | -0.8091046 |
| DRIMSeq | ENST00000375152 | 0.0114729 | 0.0051254 | 0.0002145 | ENSG00000204314 | PRRT1 | protein_coding | -1.6293289 |
| DRIMSeq | ENST00000591949 | 0.0398035 | 0.0064569 | 0.0002702 | ENSG00000205155 | PSENEN | protein_coding | 1.1716823 |
| DRIMSeq | ENST00000532358 | 0.0392027 | 0.0140341 | 0.0001958 | ENSG00000230487 | PSMG3-AS1 | lincRNA | 1.8498163 |
| DRIMSeq | ENST00000371625 | 0.0364431 | 0.0000000 | 0.0011050 | ENSG00000107317 | PTGDS | protein_coding | -1.4216030 |
| DRIMSeq | ENST00000467871 | 0.0364431 | 0.0000000 | 0.0011050 | ENSG00000107317 | PTGDS | processed_transcript | 1.4216030 |
| DRIMSeq | ENST00000497385 | 0.0319356 | 0.0050793 | 0.0002126 | ENSG00000134247 | PTGFRN | processed_transcript | 1.8693103 |
| DRIMSeq | ENST00000346049 | 0.0116080 | 0.0000000 | 0.0001446 | ENSG00000120899 | PTK2B | protein_coding | -1.1386662 |
| DRIMSeq | ENST00000521000 | 0.0116080 | 0.0000000 | 0.0001446 | ENSG00000120899 | PTK2B | retained_intron | 1.1386662 |
| DRIMSeq | ENST00000599732 | 0.0030661 | 0.0000547 | 0.0000023 | ENSG00000104960 | PTOV1 | protein_coding | -1.0554209 |
| DRIMSeq | ENST00000361574 | 0.0359426 | 0.0000000 | 0.0010810 | ENSG00000198858 | R3HDM4 | protein_coding | -1.0259227 |
| DRIMSeq | ENST00000590454 | 0.0359426 | 0.0000000 | 0.0010810 | ENSG00000198858 | R3HDM4 | nonsense_mediated_decay | 1.0259227 |
| DRIMSeq | ENST00000519348 | 0.0021685 | 0.0004886 | 0.0000102 | ENSG00000197275 | RAD54B | processed_transcript | 2.0624137 |
| DRIMSeq | ENST00000372047 | 0.0221380 | 0.0277857 | 0.0005814 | ENSG00000160271 | RALGDS | protein_coding | -1.1785559 |
| DRIMSeq | ENST00000522647 | 0.0493315 | 0.0091317 | 0.0001911 | ENSG00000184672 | RALYL | protein_coding | 1.0012023 |
| DRIMSeq | ENST00000296604 | 0.0143308 | 0.0067476 | 0.0002824 | ENSG00000164188 | RANBP3L | protein_coding | -0.6649506 |
| DRIMSeq | ENST00000515759 | 0.0143308 | 0.0078462 | 0.0003283 | ENSG00000164188 | RANBP3L | protein_coding | 0.9602182 |
| DRIMSeq | ENST00000430128 | 0.0265730 | 0.0043100 | 0.0001804 | ENSG00000228016 | RAPGEF4-AS1 | antisense | 1.7806003 |
| DRIMSeq | ENST00000493269 | 0.0236176 | 0.0067456 | 0.0001411 | ENSG00000146282 | RARS2 | processed_transcript | 1.2740397 |
| DRIMSeq | ENST00000582139 | 0.0236176 | 0.0045683 | 0.0001912 | ENSG00000167281 | RBFOX3 | protein_coding | 0.7743415 |
| DRIMSeq | ENST00000415831 | 0.0236176 | 0.0238805 | 0.0009993 | ENSG00000167281 | RBFOX3 | protein_coding | -0.6428233 |
| DRIMSeq | ENST00000270645 | 0.0168681 | 0.0000000 | 0.0002861 | ENSG00000142552 | RCN3 | protein_coding | -2.3697554 |
| DRIMSeq | ENST00000597801 | 0.0168681 | 0.0000000 | 0.0002861 | ENSG00000142552 | RCN3 | protein_coding | 2.3697554 |
| DRIMSeq | ENST00000381346 | 0.0414958 | 0.0000000 | 0.0014639 | ENSG00000072042 | RDH11 | protein_coding | 1.5702818 |
| DRIMSeq | ENST00000557331 | 0.0414958 | 0.0000000 | 0.0014639 | ENSG00000072042 | RDH11 | nonsense_mediated_decay | -1.5702818 |
| DRIMSeq | ENST00000317905 | 0.0016073 | 0.0034109 | 0.0000476 | ENSG00000108469 | RECQL5 | protein_coding | -1.3152913 |
| DRIMSeq | ENST00000579274 | 0.0016073 | 0.0052680 | 0.0000735 | ENSG00000108469 | RECQL5 | processed_transcript | 1.6897934 |
| DRIMSeq | ENST00000406246 | 0.0286343 | 0.0039963 | 0.0000836 | ENSG00000173039 | RELA | protein_coding | -1.0431225 |
| DRIMSeq | ENST00000392324 | 0.0066714 | 0.0002107 | 0.0000044 | ENSG00000064490 | RFXANK | protein_coding | -1.5535016 |
| DRIMSeq | ENST00000379359 | 0.0232151 | 0.0000000 | 0.0004904 | ENSG00000102760 | RGCC | protein_coding | -0.9493842 |
| DRIMSeq | ENST00000487837 | 0.0232151 | 0.0000000 | 0.0004904 | ENSG00000102760 | RGCC | processed_transcript | 0.9493842 |
| DRIMSeq | ENST00000332298 | 0.0386784 | 0.0145657 | 0.0006095 | ENSG00000171700 | RGS19 | protein_coding | -1.6558987 |
| DRIMSeq | ENST00000366285 | 0.0233756 | 0.0104892 | 0.0004389 | ENSG00000171792 | RHNO1 | protein_coding | 0.9650345 |
| DRIMSeq | ENST00000592247 | 0.0142257 | 0.0124079 | 0.0002596 | ENSG00000131941 | RHPN2 | retained_intron | -2.3739926 |
| DRIMSeq | ENST00000377885 | 0.0066714 | 0.0060482 | 0.0001265 | ENSG00000137075 | RNF38 | protein_coding | -0.9779660 |
| DRIMSeq | ENST00000259605 | 0.0066714 | 0.0319327 | 0.0006681 | ENSG00000137075 | RNF38 | protein_coding | 1.4323774 |
| DRIMSeq | ENST00000552502 | 0.0144000 | 0.0200157 | 0.0004188 | ENSG00000257433 | RP1-197B17.3 | lincRNA | -1.8039113 |
| DRIMSeq | ENST00000552133 | 0.0144000 | 0.0488663 | 0.0010225 | ENSG00000257433 | RP1-197B17.3 | lincRNA | 1.9876267 |
| DRIMSeq | ENST00000557551 | 0.0415266 | 0.0000000 | 0.0014807 | ENSG00000258959 | RP11-1017G21.4 | antisense | -1.0938003 |
| DRIMSeq | ENST00000557242 | 0.0415266 | 0.0000000 | 0.0014807 | ENSG00000258959 | RP11-1017G21.4 | antisense | 1.0938003 |
| DRIMSeq | ENST00000589510 | 0.0188026 | 0.0000000 | 0.0003461 | ENSG00000267193 | RP11-116O18.3 | antisense | 1.5891559 |
| DRIMSeq | ENST00000586213 | 0.0188026 | 0.0000000 | 0.0003461 | ENSG00000267193 | RP11-116O18.3 | antisense | -1.5891559 |
| DRIMSeq | ENST00000520237 | 0.0088046 | 0.0010875 | 0.0000228 | ENSG00000174093 | RP11-1407O15.2 | protein_coding | 0.9259373 |
| DRIMSeq | ENST00000564775 | 0.0228504 | 0.0000000 | 0.0004772 | ENSG00000261840 | RP11-146F11.1 | antisense | 1.4635917 |
| DRIMSeq | ENST00000568500 | 0.0228504 | 0.0000000 | 0.0004772 | ENSG00000261840 | RP11-146F11.1 | antisense | -1.4635917 |
| DRIMSeq | ENST00000560872 | 0.0460462 | 0.0095808 | 0.0001336 | ENSG00000259234 | RP11-17L5.4 | lincRNA | -0.9062493 |
| DRIMSeq | ENST00000305709 | 0.0291098 | 0.0000000 | 0.0007723 | ENSG00000170161 | RP11-262H14.4 | lincRNA | 2.9438677 |
| DRIMSeq | ENST00000467494 | 0.0291098 | 0.0000000 | 0.0007723 | ENSG00000170161 | RP11-262H14.4 | lincRNA | -2.9438677 |
| DRIMSeq | ENST00000517833 | 0.0140792 | 0.0017417 | 0.0000364 | ENSG00000247317 | RP11-273G15.2 | lincRNA | -0.8052428 |
| DRIMSeq | ENST00000303154 | 0.0337902 | 0.0054346 | 0.0001137 | ENSG00000170089 | RP11-423H2.1 | transcribed_unprocessed_pseudogene | -2.1101522 |
| DRIMSeq | ENST00000524167 | 0.0366161 | 0.0000000 | 0.0011147 | ENSG00000253452 | RP11-473J6.1 | lincRNA | 2.4356947 |
| DRIMSeq | ENST00000523748 | 0.0366161 | 0.0000000 | 0.0011147 | ENSG00000253452 | RP11-473J6.1 | lincRNA | -2.4356947 |
| DRIMSeq | ENST00000436905 | 0.0415266 | 0.0000000 | 0.0014824 | ENSG00000237457 | RP11-547I7.2 | lincRNA | 1.0051112 |
| DRIMSeq | ENST00000424735 | 0.0415266 | 0.0000000 | 0.0014824 | ENSG00000237457 | RP11-547I7.2 | lincRNA | -1.0051112 |
| DRIMSeq | ENST00000424308 | 0.0066668 | 0.0000000 | 0.0000498 | ENSG00000230812 | RP4-794H19.4 | lincRNA | 3.5843726 |
| DRIMSeq | ENST00000438195 | 0.0066668 | 0.0000000 | 0.0000498 | ENSG00000230812 | RP4-794H19.4 | lincRNA | -3.5843726 |
| DRIMSeq | ENST00000401447 | 0.0152497 | 0.0015232 | 0.0000212 | ENSG00000106399 | RPA3 | protein_coding | 2.0998392 |
| DRIMSeq | ENST00000391752 | 0.0168681 | 0.0039199 | 0.0001640 | ENSG00000170889 | RPS9 | protein_coding | 2.5631658 |
| DRIMSeq | ENST00000300738 | 0.0413406 | 0.0372409 | 0.0005195 | ENSG00000167325 | RRM1 | protein_coding | -1.0745055 |
| DRIMSeq | ENST00000429751 | 0.0114729 | 0.0005985 | 0.0000250 | ENSG00000085721 | RRN3 | protein_coding | 1.4966680 |
| DRIMSeq | ENST00000198767 | 0.0114729 | 0.0412806 | 0.0017275 | ENSG00000085721 | RRN3 | protein_coding | -0.8323631 |
| DRIMSeq | ENST00000323013 | 0.0399994 | 0.0207690 | 0.0008691 | ENSG00000189306 | RRP7A | protein_coding | -0.7115918 |
| DRIMSeq | ENST00000454950 | 0.0444097 | 0.0361915 | 0.0005048 | ENSG00000204130 | RUFY2 | protein_coding | -0.7072990 |
| DRIMSeq | ENST00000382298 | 0.0277868 | 0.0000000 | 0.0007028 | ENSG00000151835 | SACS | protein_coding | -1.2660676 |
| DRIMSeq | ENST00000476776 | 0.0277868 | 0.0000000 | 0.0007028 | ENSG00000151835 | SACS | processed_transcript | 1.2660676 |
| DRIMSeq | ENST00000270225 | 0.0196835 | 0.0018423 | 0.0000771 | ENSG00000142230 | SAE1 | protein_coding | -0.9956594 |
| DRIMSeq | ENST00000515816 | 0.0000270 | 0.0000062 | 0.0000001 | ENSG00000167100 | SAMD14 | retained_intron | 1.7959728 |
| DRIMSeq | ENST00000285206 | 0.0000270 | 0.0005107 | 0.0000107 | ENSG00000167100 | SAMD14 | protein_coding | -1.0788741 |
| DRIMSeq | ENST00000003834 | 0.0438669 | 0.0368209 | 0.0005136 | ENSG00000004139 | SARM1 | retained_intron | -0.9758894 |
| DRIMSeq | ENST00000229903 | 0.0350099 | 0.0071477 | 0.0002991 | ENSG00000112167 | SAYSD1 | protein_coding | 0.9540670 |
| DRIMSeq | ENST00000316097 | 0.0319243 | 0.0413737 | 0.0005771 | ENSG00000227500 | SCAMP4 | protein_coding | -0.7358693 |
| DRIMSeq | ENST00000397174 | 0.0008174 | 0.0000035 | 0.0000001 | ENSG00000010803 | SCMH1 | protein_coding | 3.0784708 |
| DRIMSeq | ENST00000357398 | 0.0456265 | 0.0108184 | 0.0004527 | ENSG00000136531 | SCN2A | protein_coding | 1.9057232 |
| DRIMSeq | ENST00000467651 | 0.0291518 | 0.0017500 | 0.0000244 | ENSG00000162572 | SCNN1D | processed_transcript | -3.5553000 |
| DRIMSeq | ENST00000264932 | 0.0178093 | 0.0019146 | 0.0000801 | ENSG00000073578 | SDHA | protein_coding | -1.0140144 |
| DRIMSeq | ENST00000505555 | 0.0178093 | 0.0304470 | 0.0012741 | ENSG00000073578 | SDHA | retained_intron | 1.1132052 |
| DRIMSeq | ENST00000399395 | 0.0488144 | 0.0110835 | 0.0004638 | ENSG00000100445 | SDR39U1 | protein_coding | -1.1251030 |
| DRIMSeq | ENST00000423034 | 0.0262051 | 0.0000000 | 0.0006345 | ENSG00000184640 | SEPT9 | protein_coding | 1.0114978 |
| DRIMSeq | ENST00000541152 | 0.0262051 | 0.0000000 | 0.0006345 | ENSG00000184640 | SEPT9 | protein_coding | -1.0114978 |
| DRIMSeq | ENST00000518437 | 0.0002232 | 0.0000003 | 0.0000000 | ENSG00000206573 | SETD5-AS1 | antisense | -1.5847008 |
| DRIMSeq | ENST00000400358 | 0.0064726 | 0.0004640 | 0.0000194 | ENSG00000167037 | SGSM1 | protein_coding | -0.9120369 |
| DRIMSeq | ENST00000470591 | 0.0064726 | 0.0012050 | 0.0000504 | ENSG00000167037 | SGSM1 | processed_transcript | 0.8896612 |
| DRIMSeq | ENST00000503071 | 0.0302169 | 0.0117517 | 0.0001229 | ENSG00000169247 | SH3TC2 | processed_transcript | 2.3312414 |
| DRIMSeq | ENST00000602239 | 0.0236176 | 0.0056567 | 0.0000592 | ENSG00000160410 | SHKBP1 | retained_intron | 2.5226967 |
| DRIMSeq | ENST00000378536 | 0.0018212 | 0.0000580 | 0.0000024 | ENSG00000157933 | SKI | protein_coding | -0.9287711 |
| DRIMSeq | ENST00000508416 | 0.0018212 | 0.0010707 | 0.0000448 | ENSG00000157933 | SKI | processed_transcript | 0.8883680 |
| DRIMSeq | ENST00000461616 | 0.0386784 | 0.0110564 | 0.0004627 | ENSG00000221955 | SLC12A8 | processed_transcript | -1.3056753 |
| DRIMSeq | ENST00000369626 | 0.0388082 | 0.0000000 | 0.0012464 | ENSG00000155380 | SLC16A1 | protein_coding | -1.0164828 |
| DRIMSeq | ENST00000478835 | 0.0388082 | 0.0000000 | 0.0012464 | ENSG00000155380 | SLC16A1 | processed_transcript | 1.0164828 |
| DRIMSeq | ENST00000345044 | 0.0140365 | 0.0035501 | 0.0000743 | ENSG00000133460 | SLC2A11 | protein_coding | -0.6717411 |
| DRIMSeq | ENST00000473157 | 0.0159637 | 0.0006532 | 0.0000091 | ENSG00000125520 | SLC2A4RG | processed_transcript | -2.2959060 |
| DRIMSeq | ENST00000371899 | 0.0030661 | 0.0001313 | 0.0000055 | ENSG00000160326 | SLC2A6 | protein_coding | -1.2282921 |
| DRIMSeq | ENST00000371897 | 0.0030661 | 0.0063975 | 0.0002677 | ENSG00000160326 | SLC2A6 | protein_coding | 1.1262030 |
| DRIMSeq | ENST00000343605 | 0.0470486 | 0.0000000 | 0.0018524 | ENSG00000100036 | SLC35E4 | protein_coding | -1.5092256 |
| DRIMSeq | ENST00000406566 | 0.0470486 | 0.0000000 | 0.0018524 | ENSG00000100036 | SLC35E4 | protein_coding | 1.5092256 |
| DRIMSeq | ENST00000495257 | 0.0392781 | 0.0000000 | 0.0012966 | ENSG00000157800 | SLC37A3 | processed_transcript | 0.8088996 |
| DRIMSeq | ENST00000326232 | 0.0392781 | 0.0000000 | 0.0012966 | ENSG00000157800 | SLC37A3 | protein_coding | -0.8088996 |
| DRIMSeq | ENST00000377369 | 0.0271797 | 0.0045191 | 0.0001891 | ENSG00000148482 | SLC39A12 | protein_coding | -0.9446863 |
| DRIMSeq | ENST00000377374 | 0.0271797 | 0.0200354 | 0.0008384 | ENSG00000148482 | SLC39A12 | protein_coding | 0.8230377 |
| DRIMSeq | ENST00000535347 | 0.0010311 | 0.0011647 | 0.0000244 | ENSG00000111181 | SLC6A12 | protein_coding | -1.5004534 |
| DRIMSeq | ENST00000280612 | 0.0010311 | 0.0000000 | 0.0000030 | ENSG00000151012 | SLC7A11 | protein_coding | -1.6516229 |
| DRIMSeq | ENST00000509248 | 0.0010311 | 0.0000000 | 0.0000030 | ENSG00000151012 | SLC7A11 | nonsense_mediated_decay | 1.6516229 |
| DRIMSeq | ENST00000555678 | 0.0026086 | 0.0015033 | 0.0000629 | ENSG00000155465 | SLC7A7 | retained_intron | 2.1411421 |
| DRIMSeq | ENST00000555702 | 0.0026086 | 0.0327648 | 0.0013711 | ENSG00000155465 | SLC7A7 | protein_coding | -1.7206978 |
| DRIMSeq | ENST00000452078 | 0.0388082 | 0.0000000 | 0.0012318 | ENSG00000084453 | SLCO1A2 | protein_coding | -0.8256880 |
| DRIMSeq | ENST00000463718 | 0.0388082 | 0.0000000 | 0.0012318 | ENSG00000084453 | SLCO1A2 | retained_intron | 0.8256880 |
| DRIMSeq | ENST00000506626 | 0.0019586 | 0.0002126 | 0.0000044 | ENSG00000170365 | SMAD1 | processed_transcript | 1.6353926 |
| DRIMSeq | ENST00000591914 | 0.0066714 | 0.0032406 | 0.0000452 | ENSG00000141646 | SMAD4 | protein_coding | -2.4271076 |
| DRIMSeq | ENST00000244520 | 0.0305452 | 0.0000000 | 0.0008506 | ENSG00000124562 | SNRPC | protein_coding | -1.8447219 |
| DRIMSeq | ENST00000374018 | 0.0305452 | 0.0000000 | 0.0008506 | ENSG00000124562 | SNRPC | protein_coding | 1.8447219 |
| DRIMSeq | ENST00000418788 | 0.0291518 | 0.0000000 | 0.0007829 | ENSG00000224543 | SNRPGP15 | processed_pseudogene | 2.8223554 |
| DRIMSeq | ENST00000600149 | 0.0291518 | 0.0000000 | 0.0007829 | ENSG00000224543 | SNRPGP15 | processed_pseudogene | -2.8223554 |
| DRIMSeq | ENST00000308342 | 0.0414099 | 0.0051414 | 0.0000717 | ENSG00000172803 | SNX32 | protein_coding | -0.9020106 |
| DRIMSeq | ENST00000308527 | 0.0089180 | 0.0000000 | 0.0000869 | ENSG00000173548 | SNX33 | protein_coding | 1.7959373 |
| DRIMSeq | ENST00000569152 | 0.0089180 | 0.0000000 | 0.0000869 | ENSG00000173548 | SNX33 | protein_coding | -1.7959373 |
| DRIMSeq | ENST00000206020 | 0.0471741 | 0.0000000 | 0.0018757 | ENSG00000091640 | SPAG7 | protein_coding | -0.7181095 |
| DRIMSeq | ENST00000571023 | 0.0471741 | 0.0000000 | 0.0018757 | ENSG00000091640 | SPAG7 | processed_transcript | 0.7181095 |
| DRIMSeq | ENST00000261866 | 0.0414958 | 0.0000000 | 0.0014701 | ENSG00000104133 | SPG11 | protein_coding | -0.7917938 |
| DRIMSeq | ENST00000560299 | 0.0414958 | 0.0000000 | 0.0014701 | ENSG00000104133 | SPG11 | retained_intron | 0.7917938 |
| DRIMSeq | ENST00000476377 | 0.0215993 | 0.0011817 | 0.0000247 | ENSG00000133104 | SPG20 | processed_transcript | 1.1341163 |
| DRIMSeq | ENST00000264659 | 0.0000042 | 0.0000138 | 0.0000003 | ENSG00000017373 | SRCIN1 | protein_coding | -0.8398709 |
| DRIMSeq | ENST00000581656 | 0.0000042 | 0.0001111 | 0.0000023 | ENSG00000017373 | SRCIN1 | processed_transcript | 0.9756534 |
| DRIMSeq | ENST00000586778 | 0.0343528 | 0.0078837 | 0.0001650 | ENSG00000161547 | SRSF2 | retained_intron | 1.2327994 |
| DRIMSeq | ENST00000557154 | 0.0000716 | 0.0000002 | 0.0000000 | ENSG00000100650 | SRSF5 | protein_coding | -2.0792415 |
| DRIMSeq | ENST00000348495 | 0.0287317 | 0.0474948 | 0.0019875 | ENSG00000130511 | SSBP4 | protein_coding | -1.2930314 |
| DRIMSeq | ENST00000437941 | 0.0370208 | 0.0117848 | 0.0004932 | ENSG00000117155 | SSX2IP | protein_coding | 1.0788515 |
| DRIMSeq | ENST00000361392 | 0.0013799 | 0.0000000 | 0.0000047 | ENSG00000126091 | ST3GAL3 | protein_coding | -2.1251239 |
| DRIMSeq | ENST00000361400 | 0.0013799 | 0.0000000 | 0.0000047 | ENSG00000126091 | ST3GAL3 | protein_coding | 2.1251239 |
| DRIMSeq | ENST00000444328 | 0.0366161 | 0.0293689 | 0.0012290 | ENSG00000110080 | ST3GAL4 | protein_coding | -1.0943350 |
| DRIMSeq | ENST00000393808 | 0.0236176 | 0.0018300 | 0.0000766 | ENSG00000115525 | ST3GAL5 | protein_coding | -0.9599002 |
| DRIMSeq | ENST00000492674 | 0.0005305 | 0.0000767 | 0.0000016 | ENSG00000066923 | STAG3 | retained_intron | 3.8836173 |
| DRIMSeq | ENST00000595181 | 0.0454731 | 0.0000000 | 0.0017095 | ENSG00000076944 | STXBP2 | retained_intron | 1.5092740 |
| DRIMSeq | ENST00000221283 | 0.0454731 | 0.0000000 | 0.0017095 | ENSG00000076944 | STXBP2 | protein_coding | -1.5092740 |
| DRIMSeq | ENST00000547586 | 0.0011638 | 0.0000155 | 0.0000002 | ENSG00000139531 | SUOX | protein_coding | 3.4056396 |
| DRIMSeq | ENST00000512997 | 0.0220696 | 0.0009303 | 0.0000195 | ENSG00000204176 | SYT15 | protein_coding | -1.3271994 |
| DRIMSeq | ENST00000276692 | 0.0032530 | 0.0002685 | 0.0000112 | ENSG00000147687 | TATDN1 | protein_coding | -1.4711635 |
| DRIMSeq | ENST00000520321 | 0.0032530 | 0.0242503 | 0.0010148 | ENSG00000147687 | TATDN1 | nonsense_mediated_decay | 1.7025512 |
| DRIMSeq | ENST00000258770 | 0.0066714 | 0.0003527 | 0.0000074 | ENSG00000136270 | TBRG4 | protein_coding | -1.6002542 |
| DRIMSeq | ENST00000325318 | 0.0014299 | 0.0025990 | 0.0000544 | ENSG00000213123 | TCTEX1D2 | protein_coding | -0.8966589 |
| DRIMSeq | ENST00000491186 | 0.0014299 | 0.0281887 | 0.0005898 | ENSG00000213123 | TCTEX1D2 | processed_transcript | 0.9343922 |
| DRIMSeq | ENST00000314250 | 0.0066668 | 0.0016963 | 0.0000355 | ENSG00000111077 | TENC1 | protein_coding | -0.7142071 |
| DRIMSeq | ENST00000552403 | 0.0066668 | 0.0277562 | 0.0005808 | ENSG00000111077 | TENC1 | retained_intron | 0.6986491 |
| DRIMSeq | ENST00000272438 | 0.0196835 | 0.0031051 | 0.0000650 | ENSG00000144043 | TEX261 | protein_coding | -1.0349599 |
| DRIMSeq | ENST00000374990 | 0.0187088 | 0.0020337 | 0.0000851 | ENSG00000106799 | TGFBR1 | protein_coding | 2.0244563 |
| DRIMSeq | ENST00000377627 | 0.0278433 | 0.0033315 | 0.0001394 | ENSG00000041988 | THAP3 | protein_coding | 1.7556276 |
| DRIMSeq | ENST00000368817 | 0.0187088 | 0.0000000 | 0.0003407 | ENSG00000196407 | THEM5 | protein_coding | -1.7436471 |
| DRIMSeq | ENST00000453881 | 0.0187088 | 0.0000000 | 0.0003407 | ENSG00000196407 | THEM5 | protein_coding | 1.7436471 |
| DRIMSeq | ENST00000354618 | 0.0463093 | 0.0130776 | 0.0002736 | ENSG00000054118 | THRAP3 | protein_coding | -0.6071240 |
| DRIMSeq | ENST00000452837 | 0.0256188 | 0.0096438 | 0.0001345 | ENSG00000134077 | THUMPD3 | protein_coding | -1.2211168 |
| DRIMSeq | ENST00000279263 | 0.0028413 | 0.0000073 | 0.0000001 | ENSG00000149809 | TM7SF2 | protein_coding | -1.7648473 |
| DRIMSeq | ENST00000258412 | 0.0454731 | 0.0000000 | 0.0017050 | ENSG00000135926 | TMBIM1 | protein_coding | -0.9466802 |
| DRIMSeq | ENST00000420341 | 0.0454731 | 0.0000000 | 0.0017050 | ENSG00000135926 | TMBIM1 | protein_coding | 0.9466802 |
| DRIMSeq | ENST00000481238 | 0.0415266 | 0.0128918 | 0.0005395 | ENSG00000158604 | TMED4 | protein_coding | 0.7377957 |
| DRIMSeq | ENST00000457408 | 0.0415266 | 0.0247698 | 0.0010365 | ENSG00000158604 | TMED4 | protein_coding | -0.6207155 |
| DRIMSeq | ENST00000549288 | 0.0021568 | 0.0001096 | 0.0000023 | ENSG00000134291 | TMEM106C | protein_coding | 3.0384602 |
| DRIMSeq | ENST00000382753 | 0.0098622 | 0.0007583 | 0.0000159 | ENSG00000132406 | TMEM128 | protein_coding | -1.1500210 |
| DRIMSeq | ENST00000382936 | 0.0132006 | 0.0082240 | 0.0001721 | ENSG00000168936 | TMEM129 | protein_coding | -0.7335287 |
| DRIMSeq | ENST00000480360 | 0.0132006 | 0.0430151 | 0.0009000 | ENSG00000168936 | TMEM129 | nonsense_mediated_decay | 1.0522273 |
| DRIMSeq | ENST00000537110 | 0.0228954 | 0.0047596 | 0.0001992 | ENSG00000006118 | TMEM132A | processed_transcript | 0.9809477 |
| DRIMSeq | ENST00000597370 | 0.0078481 | 0.0037711 | 0.0000395 | ENSG00000161558 | TMEM143 | nonsense_mediated_decay | 2.5173348 |
| DRIMSeq | ENST00000565468 | 0.0139758 | 0.0000000 | 0.0001929 | ENSG00000261115 | TMEM178B | protein_coding | -0.9101858 |
| DRIMSeq | ENST00000563442 | 0.0139758 | 0.0000000 | 0.0001929 | ENSG00000261115 | TMEM178B | retained_intron | 0.9101858 |
| DRIMSeq | ENST00000281017 | 0.0120253 | 0.0000000 | 0.0001544 | ENSG00000151353 | TMEM18 | protein_coding | 1.4723032 |
| DRIMSeq | ENST00000355654 | 0.0120253 | 0.0000000 | 0.0001544 | ENSG00000151353 | TMEM18 | protein_coding | -1.4723032 |
| DRIMSeq | ENST00000361906 | 0.0002232 | 0.0000023 | 0.0000000 | ENSG00000198792 | TMEM184B | protein_coding | -1.2219824 |
| DRIMSeq | ENST00000361684 | 0.0002232 | 0.0001137 | 0.0000024 | ENSG00000198792 | TMEM184B | protein_coding | 1.0403654 |
| DRIMSeq | ENST00000238788 | 0.0498511 | 0.0131848 | 0.0005517 | ENSG00000119777 | TMEM214 | protein_coding | -1.0458130 |
| DRIMSeq | ENST00000608611 | 0.0186052 | 0.0018722 | 0.0000783 | ENSG00000186501 | TMEM222 | protein_coding | -1.4103617 |
| DRIMSeq | ENST00000379299 | 0.0479198 | 0.0000000 | 0.0019386 | ENSG00000089063 | TMEM230 | protein_coding | 0.9318278 |
| DRIMSeq | ENST00000202834 | 0.0479198 | 0.0000000 | 0.0019386 | ENSG00000089063 | TMEM230 | protein_coding | -0.9318278 |
| DRIMSeq | ENST00000321196 | 0.0460462 | 0.0139210 | 0.0001942 | ENSG00000179104 | TMTC2 | protein_coding | -0.7965878 |
| DRIMSeq | ENST00000413971 | 0.0164430 | 0.0106157 | 0.0004442 | ENSG00000077097 | TOP2B | nonsense_mediated_decay | 1.2946108 |
| DRIMSeq | ENST00000272424 | 0.0077076 | 0.0010946 | 0.0000115 | ENSG00000144034 | TPRKB | protein_coding | -0.9399244 |
| DRIMSeq | ENST00000453386 | 0.0486374 | 0.0092188 | 0.0001929 | ENSG00000136527 | TRA2B | protein_coding | -0.8696028 |
| DRIMSeq | ENST00000558880 | 0.0151134 | 0.0042599 | 0.0000891 | ENSG00000131323 | TRAF3 | retained_intron | 0.8300841 |
| DRIMSeq | ENST00000412615 | 0.0079227 | 0.0002046 | 0.0000029 | ENSG00000135148 | TRAFD1 | protein_coding | -1.3175199 |
| DRIMSeq | ENST00000567312 | 0.0162533 | 0.0019006 | 0.0000265 | ENSG00000167515 | TRAPPC2L | protein_coding | -1.2429326 |
| DRIMSeq | ENST00000577426 | 0.0456265 | 0.0229534 | 0.0009605 | ENSG00000153339 | TRAPPC8 | processed_transcript | 0.6144598 |
| DRIMSeq | ENST00000441818 | 0.0263282 | 0.0026845 | 0.0000562 | ENSG00000100416 | TRMU | nonsense_mediated_decay | -0.8133667 |
| DRIMSeq | ENST00000485138 | 0.0008174 | 0.0000290 | 0.0000012 | ENSG00000165125 | TRPV6 | retained_intron | 1.7100676 |
| DRIMSeq | ENST00000463646 | 0.0008174 | 0.0001194 | 0.0000050 | ENSG00000165125 | TRPV6 | retained_intron | -1.2476065 |
| DRIMSeq | ENST00000463601 | 0.0061001 | 0.0001461 | 0.0000061 | ENSG00000103197 | TSC2 | retained_intron | 1.0686425 |
| DRIMSeq | ENST00000498097 | 0.0470082 | 0.0395465 | 0.0008275 | ENSG00000135951 | TSGA10 | processed_transcript | 0.7852308 |
| DRIMSeq | ENST00000373290 | 0.0013922 | 0.0000000 | 0.0000048 | ENSG00000099282 | TSPAN15 | protein_coding | -2.3248674 |
| DRIMSeq | ENST00000475069 | 0.0013922 | 0.0000000 | 0.0000048 | ENSG00000099282 | TSPAN15 | retained_intron | 2.3248674 |
| DRIMSeq | ENST00000508164 | 0.0098938 | 0.0004523 | 0.0000095 | ENSG00000048140 | TSPAN17 | protein_coding | -1.1291852 |
| DRIMSeq | ENST00000529221 | 0.0287317 | 0.0077394 | 0.0001619 | ENSG00000149292 | TTC12 | protein_coding | -1.7069887 |
| DRIMSeq | ENST00000472527 | 0.0319243 | 0.0031098 | 0.0000434 | ENSG00000135912 | TTLL4 | retained_intron | -1.2496065 |
| DRIMSeq | ENST00000258796 | 0.0011638 | 0.0000166 | 0.0000007 | ENSG00000136295 | TTYH3 | protein_coding | -1.1028939 |
| DRIMSeq | ENST00000400376 | 0.0011638 | 0.0011137 | 0.0000466 | ENSG00000136295 | TTYH3 | protein_coding | 1.0520785 |
| DRIMSeq | ENST00000248846 | 0.0383261 | 0.0047162 | 0.0000658 | ENSG00000128159 | TUBGCP6 | protein_coding | -0.9276863 |
| DRIMSeq | ENST00000503506 | 0.0000370 | 0.0000194 | 0.0000004 | ENSG00000198431 | TXNRD1 | protein_coding | -1.4125311 |
| DRIMSeq | ENST00000291552 | 0.0026182 | 0.0000219 | 0.0000002 | ENSG00000160201 | U2AF1 | protein_coding | -0.8800037 |
| DRIMSeq | ENST00000380276 | 0.0026182 | 0.0075896 | 0.0000794 | ENSG00000160201 | U2AF1 | protein_coding | 0.7824498 |
| DRIMSeq | ENST00000494576 | 0.0008174 | 0.0000553 | 0.0000012 | ENSG00000134882 | UBAC2 | processed_transcript | -1.4136709 |
| DRIMSeq | ENST00000460562 | 0.0008174 | 0.0145230 | 0.0003039 | ENSG00000134882 | UBAC2 | processed_transcript | 1.0985174 |
| DRIMSeq | ENST00000373910 | 0.0306250 | 0.0125094 | 0.0005235 | ENSG00000072401 | UBE2D1 | protein_coding | -0.8828690 |
| DRIMSeq | ENST00000345496 | 0.0162533 | 0.0004982 | 0.0000104 | ENSG00000184787 | UBE2G2 | protein_coding | -0.7187891 |
| DRIMSeq | ENST00000488418 | 0.0059902 | 0.0001874 | 0.0000026 | ENSG00000160087 | UBE2J2 | protein_coding | 1.3446713 |
| DRIMSeq | ENST00000360943 | 0.0286343 | 0.0029357 | 0.0000614 | ENSG00000159202 | UBE2Z | protein_coding | -0.7159087 |
| DRIMSeq | ENST00000354216 | 0.0042341 | 0.0007627 | 0.0000106 | ENSG00000198276 | UCKL1 | protein_coding | -1.0273157 |
| DRIMSeq | ENST00000509180 | 0.0026086 | 0.0244057 | 0.0005107 | ENSG00000109775 | UFSP2 | protein_coding | 1.2215603 |
| DRIMSeq | ENST00000335765 | 0.0091476 | 0.0001937 | 0.0000027 | ENSG00000109103 | UNC119 | protein_coding | -1.3518379 |
| DRIMSeq | ENST00000524574 | 0.0241927 | 0.0182382 | 0.0003816 | ENSG00000134215 | VAV3 | processed_transcript | 1.8195147 |
| DRIMSeq | ENST00000493786 | 0.0215033 | 0.0089651 | 0.0001876 | ENSG00000112715 | VEGFA | retained_intron | 1.1353827 |
| DRIMSeq | ENST00000283713 | 0.0120824 | 0.0078641 | 0.0001097 | ENSG00000136059 | VILL | protein_coding | 1.9796336 |
| DRIMSeq | ENST00000573314 | 0.0108017 | 0.0005497 | 0.0000077 | ENSG00000138614 | VWA9 | nonsense_mediated_decay | -1.6979060 |
| DRIMSeq | ENST00000261405 | 0.0479132 | 0.0000000 | 0.0019346 | ENSG00000110799 | VWF | protein_coding | 1.3836518 |
| DRIMSeq | ENST00000538635 | 0.0479132 | 0.0000000 | 0.0019346 | ENSG00000110799 | VWF | processed_transcript | -1.3836518 |
| DRIMSeq | ENST00000527986 | 0.0237692 | 0.0000000 | 0.0005301 | ENSG00000254635 | WAC-AS1 | antisense | -1.0432511 |
| DRIMSeq | ENST00000528337 | 0.0237692 | 0.0000000 | 0.0005301 | ENSG00000254635 | WAC-AS1 | antisense | 1.0432511 |
| DRIMSeq | ENST00000251289 | 0.0131100 | 0.0017262 | 0.0000361 | ENSG00000065268 | WDR18 | protein_coding | -0.9719241 |
| DRIMSeq | ENST00000395474 | 0.0066842 | 0.0000000 | 0.0000538 | ENSG00000178252 | WDR6 | protein_coding | 1.4013180 |
| DRIMSeq | ENST00000608424 | 0.0066842 | 0.0000000 | 0.0000538 | ENSG00000178252 | WDR6 | protein_coding | -1.4013180 |
| DRIMSeq | ENST00000375128 | 0.0026182 | 0.0000232 | 0.0000005 | ENSG00000136936 | XPA | protein_coding | -1.1472541 |
| DRIMSeq | ENST00000223273 | 0.0015758 | 0.0000196 | 0.0000008 | ENSG00000241127 | YAE1D1 | protein_coding | -1.0797949 |
| DRIMSeq | ENST00000469737 | 0.0015758 | 0.0161816 | 0.0006772 | ENSG00000241127 | YAE1D1 | processed_transcript | 0.9303155 |
| DRIMSeq | ENST00000376901 | 0.0281745 | 0.0050312 | 0.0001053 | ENSG00000174851 | YIF1A | protein_coding | -0.8383225 |
| DRIMSeq | ENST00000335953 | 0.0238427 | 0.0000000 | 0.0005367 | ENSG00000109906 | ZBTB16 | protein_coding | -0.8821190 |
| DRIMSeq | ENST00000545851 | 0.0238427 | 0.0000000 | 0.0005367 | ENSG00000109906 | ZBTB16 | processed_transcript | 0.8821190 |
| DRIMSeq | ENST00000262577 | 0.0438669 | 0.0000000 | 0.0016084 | ENSG00000014164 | ZC3H3 | protein_coding | -1.0340202 |
| DRIMSeq | ENST00000528401 | 0.0438669 | 0.0000000 | 0.0016084 | ENSG00000014164 | ZC3H3 | protein_coding | 1.0340202 |
| DRIMSeq | ENST00000370854 | 0.0000912 | 0.0000001 | 0.0000000 | ENSG00000171307 | ZDHHC16 | protein_coding | -2.1139856 |
| DRIMSeq | ENST00000299173 | 0.0105091 | 0.0088130 | 0.0001844 | ENSG00000166140 | ZFYVE19 | protein_coding | -0.9601799 |
| DRIMSeq | ENST00000357182 | 0.0289255 | 0.0037440 | 0.0001567 | ENSG00000163867 | ZMYM6 | protein_coding | -0.9407909 |
| DRIMSeq | ENST00000592529 | 0.0065328 | 0.0092090 | 0.0001285 | ENSG00000167384 | ZNF180 | protein_coding | -2.4128359 |
| DRIMSeq | ENST00000601993 | 0.0140365 | 0.0003465 | 0.0000073 | ENSG00000160321 | ZNF208 | protein_coding | 1.1290895 |
| DRIMSeq | ENST00000588312 | 0.0248575 | 0.0035570 | 0.0000744 | ENSG00000090612 | ZNF268 | nonsense_mediated_decay | 3.7756738 |
| DRIMSeq | ENST00000426813 | 0.0407671 | 0.0072000 | 0.0001004 | ENSG00000168661 | ZNF30 | protein_coding | -3.1193600 |
| DRIMSeq | ENST00000243643 | 0.0060303 | 0.0003722 | 0.0000078 | ENSG00000170954 | ZNF415 | protein_coding | -1.8529764 |
| DRIMSeq | ENST00000594012 | 0.0131100 | 0.0012025 | 0.0000503 | ENSG00000198521 | ZNF43 | protein_coding | -0.7952437 |
| DRIMSeq | ENST00000598288 | 0.0131100 | 0.0071325 | 0.0002985 | ENSG00000198521 | ZNF43 | protein_coding | 0.6377372 |
| DRIMSeq | ENST00000361807 | 0.0017975 | 0.0000000 | 0.0000070 | ENSG00000198298 | ZNF485 | protein_coding | -5.2613535 |
| DRIMSeq | ENST00000374435 | 0.0017975 | 0.0000000 | 0.0000070 | ENSG00000198298 | ZNF485 | protein_coding | 5.2613535 |
| DRIMSeq | ENST00000416136 | 0.0277868 | 0.0230956 | 0.0009665 | ENSG00000249709 | ZNF564 | protein_coding | 0.8884477 |
| DRIMSeq | ENST00000339282 | 0.0277868 | 0.0239762 | 0.0010033 | ENSG00000249709 | ZNF564 | protein_coding | -0.8055145 |
| DRIMSeq | ENST00000458270 | 0.0168681 | 0.0303595 | 0.0012705 | ENSG00000183309 | ZNF623 | protein_coding | 1.1627759 |
| DRIMSeq | ENST00000526926 | 0.0168681 | 0.0354094 | 0.0014818 | ENSG00000183309 | ZNF623 | protein_coding | -0.7313531 |
| DRIMSeq | ENST00000395219 | 0.0471741 | 0.0055435 | 0.0001160 | ENSG00000229809 | ZNF688 | protein_coding | -2.4200696 |
| DRIMSeq | ENST00000372507 | 0.0218151 | 0.0240719 | 0.0005037 | ENSG00000164011 | ZNF691 | protein_coding | 2.0047473 |
| DRIMSeq | ENST00000566625 | 0.0300421 | 0.0080767 | 0.0001690 | ENSG00000179965 | ZNF771 | protein_coding | 1.3272284 |
| DRIMSeq | ENST00000601857 | 0.0399994 | 0.0156517 | 0.0006550 | ENSG00000213799 | ZNF845 | protein_coding | 1.9246294 |
| DEXSeq | ENST00000464157 | 0.0147533 | 0.0007509 | 0.0000149 | ENSG00000107331 | ABCA2 | processed_transcript | 1.9741477 |
| DEXSeq | ENST00000420774 | 0.0276992 | 0.0068092 | 0.0000677 | ENSG00000214870 | AC004540.5 | lincRNA | 1.0622446 |
| DEXSeq | ENST00000417692 | 0.0280259 | 0.0036188 | 0.0000719 | ENSG00000233230 | AC079807.2 | antisense | 0.9072559 |
| DEXSeq | ENST00000497320 | 0.0438258 | 0.0097413 | 0.0001937 | ENSG00000242474 | AC093627.9 | lincRNA | -1.2075558 |
| DEXSeq | ENST00000217455 | 0.0319560 | 0.0000000 | 0.0000962 | ENSG00000101473 | ACOT8 | protein_coding | -1.0375808 |
| DEXSeq | ENST00000484975 | 0.0319560 | 0.0000000 | 0.0001476 | ENSG00000101473 | ACOT8 | retained_intron | 1.0380847 |
| DEXSeq | ENST00000373443 | 0.0311231 | 0.0133315 | 0.0000883 | ENSG00000142920 | ADC | protein_coding | -2.2437724 |
| DEXSeq | ENST00000407796 | 0.0454843 | 0.0000000 | 0.0002448 | ENSG00000142208 | AKT1 | protein_coding | -1.2131889 |
| DEXSeq | ENST00000555380 | 0.0454843 | 0.0000000 | 0.0003540 | ENSG00000142208 | AKT1 | protein_coding | 1.2138617 |
| DEXSeq | ENST00000344175 | 0.0462169 | 0.0390858 | 0.0002590 | ENSG00000204673 | AKT1S1 | protein_coding | -2.4560781 |
| DEXSeq | ENST00000358531 | 0.0161775 | 0.0020887 | 0.0000208 | ENSG00000213390 | ARHGAP19 | protein_coding | -1.5122782 |
| DEXSeq | ENST00000452522 | 0.0451945 | 0.0118982 | 0.0002365 | ENSG00000074964 | ARHGEF10L | protein_coding | -1.0469238 |
| DEXSeq | ENST00000536481 | 0.0427481 | 0.0185787 | 0.0001847 | ENSG00000110237 | ARHGEF17 | retained_intron | 0.8786830 |
| DEXSeq | ENST00000310256 | 0.0426548 | 0.0000000 | 0.0001832 | ENSG00000173409 | ARV1 | protein_coding | -0.8314768 |
| DEXSeq | ENST00000435927 | 0.0426548 | 0.0000000 | 0.0002814 | ENSG00000173409 | ARV1 | protein_coding | 0.8317807 |
| DEXSeq | ENST00000185907 | 0.0155398 | 0.0000000 | 0.0000161 | ENSG00000204147 | ASAH2B | protein_coding | 0.9648858 |
| DEXSeq | ENST00000374007 | 0.0155398 | 0.0000000 | 0.0000180 | ENSG00000204147 | ASAH2B | protein_coding | -0.9648062 |
| DEXSeq | ENST00000562396 | 0.0335650 | 0.0176287 | 0.0001168 | ENSG00000166669 | ATF7IP2 | retained_intron | 0.8761298 |
| DEXSeq | ENST00000359933 | 0.0322056 | 0.0103166 | 0.0001025 | ENSG00000066739 | ATG2B | protein_coding | -0.7748979 |
| DEXSeq | ENST00000257861 | 0.0383663 | 0.0238673 | 0.0001582 | ENSG00000135407 | AVIL | protein_coding | 0.7689175 |
| DEXSeq | ENST00000484002 | 0.0451139 | 0.0120450 | 0.0002394 | ENSG00000121753 | BAI2 | processed_transcript | 0.7017394 |
| DEXSeq | ENST00000369541 | 0.0451038 | 0.0000000 | 0.0002383 | ENSG00000116752 | BCAS2 | protein_coding | -0.9916882 |
| DEXSeq | ENST00000485021 | 0.0451038 | 0.0000000 | 0.0003410 | ENSG00000116752 | BCAS2 | processed_transcript | 0.9909855 |
| DEXSeq | ENST00000264381 | 0.0348028 | 0.0000000 | 0.0001263 | ENSG00000114200 | BCHE | protein_coding | -1.7751168 |
| DEXSeq | ENST00000540653 | 0.0348028 | 0.0000000 | 0.0002521 | ENSG00000114200 | BCHE | protein_coding | 1.7866598 |
| DEXSeq | ENST00000489183 | 0.0243025 | 0.0026552 | 0.0000528 | ENSG00000119866 | BCL11A | processed_transcript | 0.8457082 |
| DEXSeq | ENST00000409400 | 0.0458399 | 0.0392793 | 0.0002603 | ENSG00000136717 | BIN1 | protein_coding | -1.6101648 |
| DEXSeq | ENST00000533472 | 0.0487176 | 0.0148232 | 0.0002947 | ENSG00000182993 | C12orf60 | processed_transcript | 1.0527724 |
| DEXSeq | ENST00000397666 | 0.0320526 | 0.0043776 | 0.0000870 | ENSG00000130731 | C16orf13 | protein_coding | -0.8231392 |
| DEXSeq | ENST00000338401 | 0.0320526 | 0.0117331 | 0.0002332 | ENSG00000130731 | C16orf13 | protein_coding | 1.2854601 |
| DEXSeq | ENST00000565112 | 0.0133203 | 0.0005788 | 0.0000115 | ENSG00000155330 | C16orf87 | protein_coding | 1.1033509 |
| DEXSeq | ENST00000595077 | 0.0237181 | 0.0073322 | 0.0000486 | ENSG00000006015 | C19orf60 | retained_intron | 1.1632569 |
| DEXSeq | ENST00000294360 | 0.0449668 | 0.0319957 | 0.0002120 | ENSG00000162384 | C1orf123 | protein_coding | -1.0728009 |
| DEXSeq | ENST00000419612 | 0.0317633 | 0.0097016 | 0.0000964 | ENSG00000197183 | C20orf112 | protein_coding | 1.0859042 |
| DEXSeq | ENST00000359676 | 0.0317633 | 0.0203846 | 0.0002026 | ENSG00000197183 | C20orf112 | protein_coding | -0.5653623 |
| DEXSeq | ENST00000586876 | 0.0275420 | 0.0100533 | 0.0000666 | ENSG00000167434 | CA4 | nonsense_mediated_decay | 1.3687153 |
| DEXSeq | ENST00000277549 | 0.0000513 | 0.0000013 | 0.0000000 | ENSG00000148408 | CACNA1B | protein_coding | -0.9496141 |
| DEXSeq | ENST00000550804 | 0.0053229 | 0.0004956 | 0.0000033 | ENSG00000012822 | CALCOCO1 | protein_coding | -0.9834393 |
| DEXSeq | ENST00000237177 | 0.0429533 | 0.0188813 | 0.0001877 | ENSG00000118412 | CASP8AP2 | processed_transcript | -0.4755215 |
| DEXSeq | ENST00000588821 | 0.0172753 | 0.0025737 | 0.0000256 | ENSG00000183401 | CCDC159 | retained_intron | 3.1232820 |
| DEXSeq | ENST00000263102 | 0.0446211 | 0.0000000 | 0.0002170 | ENSG00000108091 | CCDC6 | protein_coding | -0.7380949 |
| DEXSeq | ENST00000518638 | 0.0446211 | 0.0000000 | 0.0003733 | ENSG00000108091 | CCDC6 | retained_intron | 0.7390301 |
| DEXSeq | ENST00000517487 | 0.0355748 | 0.0210700 | 0.0001396 | ENSG00000175305 | CCNE2 | retained_intron | 1.0277556 |
| DEXSeq | ENST00000310833 | 0.0455649 | 0.0117127 | 0.0002328 | ENSG00000174059 | CD34 | protein_coding | -0.8495901 |
| DEXSeq | ENST00000367041 | 0.0317647 | 0.0087554 | 0.0000870 | ENSG00000117335 | CD46 | protein_coding | -1.2859714 |
| DEXSeq | ENST00000476153 | 0.0451255 | 0.0215178 | 0.0002139 | ENSG00000117266 | CDK18 | retained_intron | 1.0863797 |
| DEXSeq | ENST00000514507 | 0.0263735 | 0.0030779 | 0.0000612 | ENSG00000112877 | CEP72 | processed_transcript | 1.1060809 |
| DEXSeq | ENST00000264935 | 0.0263735 | 0.0202279 | 0.0004021 | ENSG00000112877 | CEP72 | protein_coding | -0.7868682 |
| DEXSeq | ENST00000325167 | 0.0324662 | 0.0047566 | 0.0000946 | ENSG00000176108 | CHMP6 | protein_coding | -1.4373372 |
| DEXSeq | ENST00000572778 | 0.0324662 | 0.0294184 | 0.0005848 | ENSG00000176108 | CHMP6 | protein_coding | 1.1397841 |
| DEXSeq | ENST00000258930 | 0.0433468 | 0.0000000 | 0.0001980 | ENSG00000136425 | CIB2 | protein_coding | -1.5956416 |
| DEXSeq | ENST00000560618 | 0.0433468 | 0.0000000 | 0.0005258 | ENSG00000136425 | CIB2 | protein_coding | 1.6032493 |
| DEXSeq | ENST00000539413 | 0.0473317 | 0.0138134 | 0.0002746 | ENSG00000122966 | CIT | processed_transcript | 0.3665215 |
| DEXSeq | ENST00000488090 | 0.0348232 | 0.0126255 | 0.0001255 | ENSG00000119946 | CNNM1 | processed_transcript | 0.7862042 |
| DEXSeq | ENST00000462604 | 0.0004131 | 0.0000062 | 0.0000001 | ENSG00000144810 | COL8A1 | processed_transcript | 5.8725189 |
| DEXSeq | ENST00000267935 | 0.0136353 | 0.0024376 | 0.0000121 | ENSG00000140365 | COMMD4 | protein_coding | -1.2711630 |
| DEXSeq | ENST00000382395 | 0.0249714 | 0.0056425 | 0.0000561 | ENSG00000137449 | CPEB2 | protein_coding | -0.8510152 |
| DEXSeq | ENST00000550030 | 0.0344089 | 0.0185847 | 0.0001232 | ENSG00000169372 | CRADD | processed_transcript | 1.1836891 |
| DEXSeq | ENST00000332896 | 0.0344089 | 0.0477301 | 0.0003163 | ENSG00000169372 | CRADD | protein_coding | -1.1626318 |
| DEXSeq | ENST00000468839 | 0.0364583 | 0.0145767 | 0.0001449 | ENSG00000007545 | CRAMP1L | retained_intron | 1.0440394 |
| DEXSeq | ENST00000482691 | 0.0357863 | 0.0209287 | 0.0001387 | ENSG00000163703 | CRELD1 | retained_intron | 1.0035662 |
| DEXSeq | ENST00000513708 | 0.0486718 | 0.0147488 | 0.0002932 | ENSG00000230561 | CTC-228N24.1 | lincRNA | 0.9456918 |
| DEXSeq | ENST00000415461 | 0.0161189 | 0.0010606 | 0.0000211 | ENSG00000085733 | CTTN | protein_coding | 1.1305303 |
| DEXSeq | ENST00000577830 | 0.0451452 | 0.0223123 | 0.0002218 | ENSG00000180891 | CUEDC1 | protein_coding | -0.7587885 |
| DEXSeq | ENST00000490926 | 0.0141497 | 0.0007027 | 0.0000140 | ENSG00000114395 | CYB561D2 | processed_transcript | 1.4195431 |
| DEXSeq | ENST00000573984 | 0.0384621 | 0.0078801 | 0.0001567 | ENSG00000167740 | CYB5D2 | protein_coding | 0.8769765 |
| DEXSeq | ENST00000491083 | 0.0479358 | 0.0141088 | 0.0002805 | ENSG00000146122 | DAAM2 | processed_transcript | 0.9889428 |
| DEXSeq | ENST00000261891 | 0.0450867 | 0.0221714 | 0.0002204 | ENSG00000035664 | DAPK2 | protein_coding | -1.2278918 |
| DEXSeq | ENST00000446987 | 0.0453143 | 0.0337627 | 0.0002237 | ENSG00000136271 | DDX56 | nonsense_mediated_decay | -0.8393622 |
| DEXSeq | ENST00000220764 | 0.0282515 | 0.0036830 | 0.0000732 | ENSG00000104325 | DECR1 | protein_coding | -1.4658881 |
| DEXSeq | ENST00000521668 | 0.0282515 | 0.0071674 | 0.0001425 | ENSG00000104325 | DECR1 | processed_transcript | 1.3245404 |
| DEXSeq | ENST00000537639 | 0.0159772 | 0.0009124 | 0.0000181 | ENSG00000146966 | DENND2A | protein_coding | -5.1299661 |
| DEXSeq | ENST00000485359 | 0.0179888 | 0.0013846 | 0.0000275 | ENSG00000198837 | DENND4B | retained_intron | 1.0291223 |
| DEXSeq | ENST00000409775 | 0.0463127 | 0.0265714 | 0.0002641 | ENSG00000105928 | DFNA5 | protein_coding | -1.7725712 |
| DEXSeq | ENST00000332324 | 0.0458997 | 0.0127111 | 0.0002527 | ENSG00000185000 | DGAT1 | protein_coding | -0.7997587 |
| DEXSeq | ENST00000431497 | 0.0452008 | 0.0236873 | 0.0002354 | ENSG00000231764 | DLX6-AS1 | antisense | -0.9415012 |
| DEXSeq | ENST00000592152 | 0.0199632 | 0.0051304 | 0.0000340 | ENSG00000187775 | DNAH17 | processed_transcript | -1.9314506 |
| DEXSeq | ENST00000473051 | 0.0129596 | 0.0010297 | 0.0000102 | ENSG00000148719 | DNAJB12 | retained_intron | 0.9811873 |
| DEXSeq | ENST00000220496 | 0.0435310 | 0.0197841 | 0.0001966 | ENSG00000104129 | DNAJC17 | protein_coding | -0.8251132 |
| DEXSeq | ENST00000553645 | 0.0356380 | 0.0070801 | 0.0001407 | ENSG00000119661 | DNAL1 | protein_coding | -0.4892015 |
| DEXSeq | ENST00000555919 | 0.0356380 | 0.0329027 | 0.0006541 | ENSG00000119661 | DNAL1 | protein_coding | 0.6231266 |
| DEXSeq | ENST00000559585 | 0.0178800 | 0.0041954 | 0.0000278 | ENSG00000134146 | DPH6 | processed_transcript | -1.4653917 |
| DEXSeq | ENST00000394389 | 0.0450704 | 0.0108577 | 0.0002158 | ENSG00000161326 | DUSP14 | protein_coding | -1.0344867 |
| DEXSeq | ENST00000558813 | 0.0014534 | 0.0000180 | 0.0000004 | ENSG00000128951 | DUT | protein_coding | -0.8777551 |
| DEXSeq | ENST00000561350 | 0.0014534 | 0.0000224 | 0.0000004 | ENSG00000128951 | DUT | processed_transcript | 1.6189405 |
| DEXSeq | ENST00000342725 | 0.0043285 | 0.0002364 | 0.0000024 | ENSG00000088881 | EBF4 | protein_coding | -3.3065357 |
| DEXSeq | ENST00000521662 | 0.0423790 | 0.0182077 | 0.0001810 | ENSG00000120533 | ENY2 | protein_coding | -0.5334053 |
| DEXSeq | ENST00000460133 | 0.0160975 | 0.0018786 | 0.0000187 | ENSG00000158220 | ESYT3 | processed_transcript | -0.7557857 |
| DEXSeq | ENST00000468103 | 0.0160975 | 0.0054225 | 0.0000539 | ENSG00000158220 | ESYT3 | retained_intron | 0.9019386 |
| DEXSeq | ENST00000374280 | 0.0277868 | 0.0033464 | 0.0000665 | ENSG00000158008 | EXTL1 | protein_coding | -1.1324178 |
| DEXSeq | ENST00000470037 | 0.0277868 | 0.0216676 | 0.0004307 | ENSG00000158008 | EXTL1 | processed_transcript | 1.0337283 |
| DEXSeq | ENST00000588067 | 0.0161643 | 0.0010837 | 0.0000215 | ENSG00000161682 | FAM171A2 | nonsense_mediated_decay | 0.9247354 |
| DEXSeq | ENST00000293443 | 0.0161643 | 0.0428283 | 0.0008514 | ENSG00000161682 | FAM171A2 | protein_coding | -0.6997977 |
| DEXSeq | ENST00000494172 | 0.0335643 | 0.0055427 | 0.0001102 | ENSG00000168754 | FAM178B | retained_intron | 1.8965394 |
| DEXSeq | ENST00000520074 | 0.0335643 | 0.0129999 | 0.0002584 | ENSG00000168754 | FAM178B | processed_transcript | -1.2536785 |
| DEXSeq | ENST00000564424 | 0.0294168 | 0.0116143 | 0.0000770 | ENSG00000172775 | FAM192A | protein_coding | 1.1892810 |
| DEXSeq | ENST00000310542 | 0.0441600 | 0.0101996 | 0.0002028 | ENSG00000173295 | FAM86B3P | processed_transcript | -0.9547738 |
| DEXSeq | ENST00000252530 | 0.0333460 | 0.0177621 | 0.0001177 | ENSG00000130244 | FAM98C | protein_coding | -1.3485450 |
| DEXSeq | ENST00000467237 | 0.0498514 | 0.0318231 | 0.0003163 | ENSG00000164896 | FASTK | retained_intron | 0.9460292 |
| DEXSeq | ENST00000444207 | 0.0352425 | 0.0199542 | 0.0001322 | ENSG00000100225 | FBXO7 | protein_coding | 0.8202126 |
| DEXSeq | ENST00000586042 | 0.0316303 | 0.0043984 | 0.0000874 | ENSG00000070388 | FGF22 | protein_coding | -2.0481687 |
| DEXSeq | ENST00000602661 | 0.0334832 | 0.0112249 | 0.0001116 | ENSG00000106692 | FKTN | protein_coding | -1.0359112 |
| DEXSeq | ENST00000330753 | 0.0454147 | 0.0228969 | 0.0002276 | ENSG00000185070 | FLRT2 | protein_coding | -0.8054658 |
| DEXSeq | ENST00000570759 | 0.0014971 | 0.0000335 | 0.0000003 | ENSG00000059122 | FLYWCH1 | processed_transcript | 0.7968922 |
| DEXSeq | ENST00000478432 | 0.0453622 | 0.0351508 | 0.0002329 | ENSG00000131781 | FMO5 | processed_transcript | -0.7960449 |
| DEXSeq | ENST00000479318 | 0.0028476 | 0.0001803 | 0.0000012 | ENSG00000149531 | FRG1B | nonsense_mediated_decay | 1.1282478 |
| DEXSeq | ENST00000358464 | 0.0028476 | 0.0231283 | 0.0001533 | ENSG00000149531 | FRG1B | protein_coding | -0.8542483 |
| DEXSeq | ENST00000439954 | 0.0028476 | 0.0293734 | 0.0001946 | ENSG00000149531 | FRG1B | protein_coding | -0.7579418 |
| DEXSeq | ENST00000254108 | 0.0456188 | 0.0498530 | 0.0002478 | ENSG00000089280 | FUS | protein_coding | -0.7212387 |
| DEXSeq | ENST00000559095 | 0.0490621 | 0.0154766 | 0.0003077 | ENSG00000156958 | GALK2 | processed_transcript | 0.6609706 |
| DEXSeq | ENST00000473184 | 0.0353521 | 0.0204113 | 0.0001353 | ENSG00000167491 | GATAD2A | processed_transcript | 0.9279694 |
| DEXSeq | ENST00000377960 | 0.0495136 | 0.0153731 | 0.0003056 | ENSG00000122694 | GLIPR2 | protein_coding | -1.9226815 |
| DEXSeq | ENST00000246802 | 0.0384642 | 0.0000000 | 0.0001576 | ENSG00000105373 | GLTSCR2 | protein_coding | -0.5802323 |
| DEXSeq | ENST00000599253 | 0.0384642 | 0.0000000 | 0.0001904 | ENSG00000105373 | GLTSCR2 | processed_transcript | 0.5800481 |
| DEXSeq | ENST00000264039 | 0.0139983 | 0.0000000 | 0.0000131 | ENSG00000063660 | GPC1 | protein_coding | -0.6569467 |
| DEXSeq | ENST00000426280 | 0.0139983 | 0.0000000 | 0.0000145 | ENSG00000063660 | GPC1 | protein_coding | 0.6569540 |
| DEXSeq | ENST00000397088 | 0.0139404 | 0.0012807 | 0.0000127 | ENSG00000164850 | GPER1 | protein_coding | -1.3135895 |
| DEXSeq | ENST00000489654 | 0.0330692 | 0.0168755 | 0.0001118 | ENSG00000197448 | GSTK1 | retained_intron | 0.5678089 |
| DEXSeq | ENST00000448539 | 0.0313834 | 0.0088061 | 0.0000875 | ENSG00000119041 | GTF3C3 | nonsense_mediated_decay | 1.0713327 |
| DEXSeq | ENST00000484971 | 0.0098012 | 0.0006814 | 0.0000068 | ENSG00000100226 | GTPBP1 | nonsense_mediated_decay | 1.3730799 |
| DEXSeq | ENST00000506842 | 0.0022340 | 0.0000887 | 0.0000009 | ENSG00000138642 | HERC6 | retained_intron | 1.1783772 |
| DEXSeq | ENST00000376809 | 0.0000000 | 0.0000000 | 0.0000000 | ENSG00000206503 | HLA-A | protein_coding | 1.1780353 |
| DEXSeq | ENST00000376802 | 0.0000000 | 0.0000000 | 0.0000000 | ENSG00000206503 | HLA-A | protein_coding | -1.1781719 |
| DEXSeq | ENST00000450735 | 0.0453722 | 0.0346513 | 0.0002296 | ENSG00000103942 | HOMER2 | protein_coding | -0.6753980 |
| DEXSeq | ENST00000560374 | 0.0453722 | 0.0364129 | 0.0002413 | ENSG00000103942 | HOMER2 | processed_transcript | 0.5987107 |
| DEXSeq | ENST00000438032 | 0.0234422 | 0.0073342 | 0.0000486 | ENSG00000127483 | HP1BP3 | protein_coding | 0.8346948 |
| DEXSeq | ENST00000487117 | 0.0234422 | 0.0180726 | 0.0001198 | ENSG00000127483 | HP1BP3 | processed_transcript | 0.9082637 |
| DEXSeq | ENST00000358290 | 0.0008015 | 0.0000070 | 0.0000001 | ENSG00000198189 | HSD17B11 | protein_coding | -1.0658488 |
| DEXSeq | ENST00000508413 | 0.0008015 | 0.0000157 | 0.0000003 | ENSG00000198189 | HSD17B11 | processed_transcript | 2.1147787 |
| DEXSeq | ENST00000519735 | 0.0182641 | 0.0014512 | 0.0000288 | ENSG00000104365 | IKBKB | protein_coding | -0.8334304 |
| DEXSeq | ENST00000256108 | 0.0134361 | 0.0000000 | 0.0000113 | ENSG00000133731 | IMPA1 | protein_coding | -1.0413753 |
| DEXSeq | ENST00000522997 | 0.0134361 | 0.0000000 | 0.0000214 | ENSG00000133731 | IMPA1 | protein_coding | 1.0426950 |
| DEXSeq | ENST00000562918 | 0.0440552 | 0.0205696 | 0.0002045 | ENSG00000140678 | ITGAX | processed_transcript | 1.2090699 |
| DEXSeq | ENST00000366758 | 0.0441987 | 0.0104281 | 0.0002073 | ENSG00000081692 | JMJD4 | protein_coding | -1.8522198 |
| DEXSeq | ENST00000472869 | 0.0450975 | 0.0113124 | 0.0002249 | ENSG00000135750 | KCNK1 | processed_transcript | 1.1831023 |
| DEXSeq | ENST00000366621 | 0.0450975 | 0.0278237 | 0.0005531 | ENSG00000135750 | KCNK1 | protein_coding | -0.5723548 |
| DEXSeq | ENST00000479179 | 0.0202088 | 0.0032616 | 0.0000324 | ENSG00000168301 | KCTD6 | protein_coding | 0.6912096 |
| DEXSeq | ENST00000470573 | 0.0242224 | 0.0051124 | 0.0000508 | ENSG00000117139 | KDM5B | processed_transcript | 1.0050487 |
| DEXSeq | ENST00000327300 | 0.0320988 | 0.0000000 | 0.0000959 | ENSG00000121774 | KHDRBS1 | protein_coding | -0.8688409 |
| DEXSeq | ENST00000484270 | 0.0320988 | 0.0000000 | 0.0001197 | ENSG00000121774 | KHDRBS1 | processed_transcript | 0.8689331 |
| DEXSeq | ENST00000460881 | 0.0453839 | 0.0365206 | 0.0002420 | ENSG00000149633 | KIAA1755 | retained_intron | 0.7490998 |
| DEXSeq | ENST00000443149 | 0.0208149 | 0.0061245 | 0.0000406 | ENSG00000183354 | KIAA2026 | processed_transcript | 1.0242627 |
| DEXSeq | ENST00000436015 | 0.0208149 | 0.0067970 | 0.0000450 | ENSG00000183354 | KIAA2026 | nonsense_mediated_decay | 0.8340028 |
| DEXSeq | ENST00000534023 | 0.0485810 | 0.0296840 | 0.0002950 | ENSG00000174996 | KLC2 | retained_intron | 1.7323931 |
| DEXSeq | ENST00000347162 | 0.0352255 | 0.0000000 | 0.0001304 | ENSG00000137171 | KLC4 | protein_coding | -1.0111739 |
| DEXSeq | ENST00000463168 | 0.0352255 | 0.0000000 | 0.0001609 | ENSG00000137171 | KLC4 | retained_intron | 1.0115485 |
| DEXSeq | ENST00000497048 | 0.0452318 | 0.0112899 | 0.0002244 | ENSG00000136826 | KLF4 | retained_intron | 1.7661708 |
| DEXSeq | ENST00000392647 | 0.0239556 | 0.0000000 | 0.0000514 | ENSG00000213160 | KLHL23 | protein_coding | 1.2762743 |
| DEXSeq | ENST00000437875 | 0.0239556 | 0.0000000 | 0.0000892 | ENSG00000213160 | KLHL23 | protein_coding | -1.2798298 |
| DEXSeq | ENST00000304613 | 0.0466166 | 0.0000000 | 0.0002681 | ENSG00000171798 | KNDC1 | protein_coding | -0.7465795 |
| DEXSeq | ENST00000368571 | 0.0466166 | 0.0000000 | 0.0003490 | ENSG00000171798 | KNDC1 | protein_coding | 0.7463763 |
| DEXSeq | ENST00000418974 | 0.0262216 | 0.0060553 | 0.0000602 | ENSG00000235398 | LINC00623 | lincRNA | 1.9251008 |
| DEXSeq | ENST00000429464 | 0.0157759 | 0.0009401 | 0.0000187 | ENSG00000235597 | LINC01102 | lincRNA | 1.1466160 |
| DEXSeq | ENST00000478551 | 0.0336186 | 0.0055934 | 0.0001112 | ENSG00000163818 | LZTFL1 | retained_intron | 1.1061921 |
| DEXSeq | ENST00000292599 | 0.0277925 | 0.0069702 | 0.0000693 | ENSG00000161021 | MAML1 | protein_coding | -0.9090478 |
| DEXSeq | ENST00000507385 | 0.0277925 | 0.0194896 | 0.0001937 | ENSG00000161021 | MAML1 | retained_intron | 2.5778328 |
| DEXSeq | ENST00000330651 | 0.0281408 | 0.0000000 | 0.0000715 | ENSG00000185386 | MAPK11 | protein_coding | -0.7526864 |
| DEXSeq | ENST00000449719 | 0.0281408 | 0.0000000 | 0.0001592 | ENSG00000185386 | MAPK11 | protein_coding | 0.7496687 |
| DEXSeq | ENST00000358935 | 0.0029482 | 0.0000732 | 0.0000015 | ENSG00000198060 | MARCH5 | protein_coding | -0.7024309 |
| DEXSeq | ENST00000251472 | 0.0324437 | 0.0051159 | 0.0001017 | ENSG00000105613 | MAST1 | protein_coding | -0.7824267 |
| DEXSeq | ENST00000586884 | 0.0264680 | 0.0031218 | 0.0000621 | ENSG00000141644 | MBD1 | retained_intron | 0.6789477 |
| DEXSeq | ENST00000457839 | 0.0264680 | 0.0038012 | 0.0000756 | ENSG00000141644 | MBD1 | protein_coding | -0.8624020 |
| DEXSeq | ENST00000301327 | 0.0314482 | 0.0042169 | 0.0000838 | ENSG00000167700 | MFSD3 | protein_coding | -0.9590045 |
| DEXSeq | ENST00000591673 | 0.0463866 | 0.0130188 | 0.0002588 | ENSG00000102858 | MGRN1 | processed_transcript | 0.7631349 |
| DEXSeq | ENST00000309340 | 0.0446905 | 0.0217545 | 0.0002162 | ENSG00000099875 | MKNK2 | protein_coding | 1.4989768 |
| DEXSeq | ENST00000591601 | 0.0446905 | 0.0410381 | 0.0004079 | ENSG00000099875 | MKNK2 | protein_coding | -1.4612855 |
| DEXSeq | ENST00000566203 | 0.0202601 | 0.0017607 | 0.0000350 | ENSG00000126005 | MMP24-AS1 | antisense | 0.9306040 |
| DEXSeq | ENST00000258169 | 0.0437149 | 0.0000000 | 0.0001942 | ENSG00000135698 | MPHOSPH6 | protein_coding | -0.9663268 |
| DEXSeq | ENST00000569021 | 0.0437149 | 0.0000000 | 0.0002069 | ENSG00000135698 | MPHOSPH6 | protein_coding | 0.9663316 |
| DEXSeq | ENST00000367034 | 0.0477476 | 0.0000000 | 0.0002806 | ENSG00000112110 | MRPL18 | protein_coding | -0.7958483 |
| DEXSeq | ENST00000479638 | 0.0477476 | 0.0000000 | 0.0003559 | ENSG00000112110 | MRPL18 | processed_transcript | 0.7956226 |
| DEXSeq | ENST00000594784 | 0.0488168 | 0.0441963 | 0.0002929 | ENSG00000141971 | MVB12A | protein_coding | -4.0292650 |
| DEXSeq | ENST00000351429 | 0.0474423 | 0.0137867 | 0.0002741 | ENSG00000156239 | N6AMT1 | protein_coding | 1.1323961 |
| DEXSeq | ENST00000534548 | 0.0433072 | 0.0197899 | 0.0001967 | ENSG00000151503 | NCAPD3 | protein_coding | -0.9300633 |
| DEXSeq | ENST00000420993 | 0.0196601 | 0.0016353 | 0.0000325 | ENSG00000025770 | NCAPH2 | protein_coding | -0.8335836 |
| DEXSeq | ENST00000522048 | 0.0196601 | 0.0088839 | 0.0001766 | ENSG00000025770 | NCAPH2 | retained_intron | 0.5340252 |
| DEXSeq | ENST00000395698 | 0.0196601 | 0.0391744 | 0.0007788 | ENSG00000025770 | NCAPH2 | protein_coding | 0.8629591 |
| DEXSeq | ENST00000436750 | 0.0333409 | 0.0000000 | 0.0001144 | ENSG00000154328 | NEIL2 | protein_coding | -0.9867391 |
| DEXSeq | ENST00000284503 | 0.0333409 | 0.0000000 | 0.0001307 | ENSG00000154328 | NEIL2 | protein_coding | 0.9867589 |
| DEXSeq | ENST00000559571 | 0.0251406 | 0.0055559 | 0.0000552 | ENSG00000140157 | NIPA2 | processed_transcript | 1.0207247 |
| DEXSeq | ENST00000572559 | 0.0314928 | 0.0170480 | 0.0000847 | ENSG00000153406 | NMRAL1 | processed_transcript | 1.0505946 |
| DEXSeq | ENST00000404295 | 0.0314928 | 0.0462607 | 0.0002299 | ENSG00000153406 | NMRAL1 | protein_coding | -1.5998567 |
| DEXSeq | ENST00000464284 | 0.0330017 | 0.0056546 | 0.0001124 | ENSG00000198929 | NOS1AP | protein_coding | 0.5826599 |
| DEXSeq | ENST00000425241 | 0.0325846 | 0.0094669 | 0.0000941 | ENSG00000177463 | NR2C2 | protein_coding | -0.9041961 |
| DEXSeq | ENST00000352171 | 0.0455288 | 0.0000000 | 0.0002439 | ENSG00000078618 | NRD1 | protein_coding | -0.7837824 |
| DEXSeq | ENST00000464385 | 0.0455288 | 0.0000000 | 0.0002797 | ENSG00000078618 | NRD1 | processed_transcript | 0.7838598 |
| DEXSeq | ENST00000252594 | 0.0156008 | 0.0009878 | 0.0000196 | ENSG00000130305 | NSUN5 | protein_coding | 2.3993739 |
| DEXSeq | ENST00000438747 | 0.0156008 | 0.0029327 | 0.0000583 | ENSG00000130305 | NSUN5 | protein_coding | -1.7201404 |
| DEXSeq | ENST00000279206 | 0.0363936 | 0.0219619 | 0.0001455 | ENSG00000149761 | NUDT22 | protein_coding | -0.8085654 |
| DEXSeq | ENST00000550459 | 0.0464329 | 0.0000000 | 0.0002659 | ENSG00000075188 | NUP37 | protein_coding | 1.0369605 |
| DEXSeq | ENST00000552283 | 0.0464329 | 0.0000000 | 0.0003255 | ENSG00000075188 | NUP37 | protein_coding | -1.0374196 |
| DEXSeq | ENST00000379123 | 0.0435576 | 0.0195798 | 0.0001946 | ENSG00000007372 | PAX6 | protein_coding | 0.8657646 |
| DEXSeq | ENST00000440052 | 0.0422229 | 0.0089654 | 0.0001782 | ENSG00000238197 | PAXBP1-AS1 | antisense | 1.0411781 |
| DEXSeq | ENST00000498822 | 0.0495940 | 0.0314123 | 0.0003122 | ENSG00000090097 | PCBP4 | retained_intron | 1.0956257 |
| DEXSeq | ENST00000308824 | 0.0353701 | 0.0132631 | 0.0001318 | ENSG00000203880 | PCMTD2 | protein_coding | -0.7405277 |
| DEXSeq | ENST00000490749 | 0.0492048 | 0.0151549 | 0.0003013 | ENSG00000186642 | PDE2A | retained_intron | 0.8716561 |
| DEXSeq | ENST00000334456 | 0.0492048 | 0.0188396 | 0.0003745 | ENSG00000186642 | PDE2A | protein_coding | -0.6705194 |
| DEXSeq | ENST00000494559 | 0.0199293 | 0.0016330 | 0.0000325 | ENSG00000121440 | PDZRN3 | protein_coding | -0.5018944 |
| DEXSeq | ENST00000488858 | 0.0000000 | 0.0000000 | 0.0000000 | ENSG00000162734 | PEA15 | processed_transcript | 0.3807076 |
| DEXSeq | ENST00000360472 | 0.0000000 | 0.0000000 | 0.5342639 | ENSG00000162734 | PEA15 | protein_coding | 0.2550591 |
| DEXSeq | ENST00000472750 | 0.0494666 | 0.0462597 | 0.0003065 | ENSG00000162735 | PEX19 | nonsense_mediated_decay | 0.8011748 |
| DEXSeq | ENST00000413079 | 0.0014836 | 0.0000295 | 0.0000003 | ENSG00000067057 | PFKP | protein_coding | 1.5842582 |
| DEXSeq | ENST00000381072 | 0.0014836 | 0.0005299 | 0.0000053 | ENSG00000067057 | PFKP | protein_coding | 1.3274107 |
| DEXSeq | ENST00000381125 | 0.0014836 | 0.0010914 | 0.0000108 | ENSG00000067057 | PFKP | protein_coding | -1.3933861 |
| DEXSeq | ENST00000480008 | 0.0317302 | 0.0000000 | 0.0000979 | ENSG00000130024 | PHF10 | retained_intron | -0.6118879 |
| DEXSeq | ENST00000366780 | 0.0317302 | 0.0000000 | 0.0001148 | ENSG00000130024 | PHF10 | protein_coding | 0.6121189 |
| DEXSeq | ENST00000356976 | 0.0322408 | 0.0050438 | 0.0001003 | ENSG00000100151 | PICK1 | protein_coding | -0.8539558 |
| DEXSeq | ENST00000263967 | 0.0152479 | 0.0008140 | 0.0000162 | ENSG00000121879 | PIK3CA | protein_coding | -0.5358963 |
| DEXSeq | ENST00000465571 | 0.0313468 | 0.0044369 | 0.0000882 | ENSG00000124181 | PLCG1 | processed_transcript | 0.6278127 |
| DEXSeq | ENST00000326631 | 0.0164628 | 0.0022482 | 0.0000223 | ENSG00000104886 | PLEKHJ1 | protein_coding | -0.8360952 |
| DEXSeq | ENST00000282903 | 0.0229056 | 0.0046638 | 0.0000464 | ENSG00000152952 | PLOD2 | protein_coding | -1.4489120 |
| DEXSeq | ENST00000360060 | 0.0229056 | 0.0162240 | 0.0001613 | ENSG00000152952 | PLOD2 | protein_coding | 1.1973909 |
| DEXSeq | ENST00000483373 | 0.0460593 | 0.0260827 | 0.0002593 | ENSG00000120756 | PLS1 | protein_coding | 1.4641630 |
| DEXSeq | ENST00000354952 | 0.0194754 | 0.0016441 | 0.0000327 | ENSG00000114698 | PLSCR4 | protein_coding | -1.7585001 |
| DEXSeq | ENST00000593887 | 0.0201333 | 0.0056240 | 0.0000373 | ENSG00000062822 | POLD1 | protein_coding | 1.9595978 |
| DEXSeq | ENST00000312419 | 0.0199802 | 0.0054324 | 0.0000360 | ENSG00000175482 | POLD4 | protein_coding | -1.4902752 |
| DEXSeq | ENST00000503371 | 0.0349325 | 0.0192580 | 0.0001276 | ENSG00000130997 | POLN | processed_transcript | 0.7577688 |
| DEXSeq | ENST00000344697 | 0.0494364 | 0.0000000 | 0.0003125 | ENSG00000144647 | POMGNT2 | protein_coding | 1.0213761 |
| DEXSeq | ENST00000441964 | 0.0494364 | 0.0000000 | 0.0003264 | ENSG00000144647 | POMGNT2 | protein_coding | -1.0214010 |
| DEXSeq | ENST00000455780 | 0.0169233 | 0.0024372 | 0.0000242 | ENSG00000127125 | PPCS | protein_coding | -1.4520503 |
| DEXSeq | ENST00000301242 | 0.0462977 | 0.0000000 | 0.0002560 | ENSG00000167641 | PPP1R14A | protein_coding | -1.5910586 |
| DEXSeq | ENST00000587515 | 0.0462977 | 0.0000000 | 0.0003908 | ENSG00000167641 | PPP1R14A | protein_coding | 1.5893270 |
| DEXSeq | ENST00000590895 | 0.0175258 | 0.0025675 | 0.0000255 | ENSG00000122490 | PQLC1 | processed_transcript | 1.1736204 |
| DEXSeq | ENST00000375155 | 0.0478142 | 0.0141918 | 0.0002821 | ENSG00000040487 | PQLC2 | protein_coding | -0.9252251 |
| DEXSeq | ENST00000592741 | 0.0126947 | 0.0014184 | 0.0000094 | ENSG00000130175 | PRKCSH | protein_coding | -0.8235793 |
| DEXSeq | ENST00000548436 | 0.0343604 | 0.0122870 | 0.0001221 | ENSG00000110844 | PRPF40B | retained_intron | 0.8471639 |
| DEXSeq | ENST00000591949 | 0.0376767 | 0.0076724 | 0.0001525 | ENSG00000205155 | PSENEN | protein_coding | 1.2248354 |
| DEXSeq | ENST00000338910 | 0.0268600 | 0.0064028 | 0.0000636 | ENSG00000121390 | PSPC1 | protein_coding | -0.6958642 |
| DEXSeq | ENST00000492741 | 0.0268600 | 0.0468112 | 0.0004653 | ENSG00000121390 | PSPC1 | nonsense_mediated_decay | 0.5017319 |
| DEXSeq | ENST00000308020 | 0.0457097 | 0.0350795 | 0.0002325 | ENSG00000174915 | PTDSS2 | protein_coding | -0.8358544 |
| DEXSeq | ENST00000346049 | 0.0332889 | 0.0000000 | 0.0001117 | ENSG00000120899 | PTK2B | protein_coding | -1.2428583 |
| DEXSeq | ENST00000521000 | 0.0332889 | 0.0000000 | 0.0001274 | ENSG00000120899 | PTK2B | retained_intron | 1.2431292 |
| DEXSeq | ENST00000598632 | 0.0395959 | 0.0082600 | 0.0001642 | ENSG00000104960 | PTOV1 | retained_intron | 0.8287403 |
| DEXSeq | ENST00000599732 | 0.0395959 | 0.0209965 | 0.0004174 | ENSG00000104960 | PTOV1 | protein_coding | -1.0939320 |
| DEXSeq | ENST00000597793 | 0.0395959 | 0.0242355 | 0.0004818 | ENSG00000104960 | PTOV1 | retained_intron | 0.8343388 |
| DEXSeq | ENST00000555256 | 0.0435727 | 0.0196948 | 0.0001958 | ENSG00000139998 | RAB15 | retained_intron | 0.8054068 |
| DEXSeq | ENST00000297592 | 0.0357553 | 0.0140292 | 0.0001394 | ENSG00000197275 | RAD54B | protein_coding | -1.0629807 |
| DEXSeq | ENST00000296604 | 0.0199981 | 0.0018373 | 0.0000365 | ENSG00000164188 | RANBP3L | protein_coding | -0.6729579 |
| DEXSeq | ENST00000515759 | 0.0199981 | 0.0093508 | 0.0001859 | ENSG00000164188 | RANBP3L | protein_coding | 0.9884384 |
| DEXSeq | ENST00000430128 | 0.0442653 | 0.0102789 | 0.0002043 | ENSG00000228016 | RAPGEF4-AS1 | antisense | 2.0183340 |
| DEXSeq | ENST00000486790 | 0.0352640 | 0.0202291 | 0.0001340 | ENSG00000180198 | RCC1 | protein_coding | 2.3069718 |
| DEXSeq | ENST00000317905 | 0.0022132 | 0.0001154 | 0.0000008 | ENSG00000108469 | RECQL5 | protein_coding | -1.2920213 |
| DEXSeq | ENST00000392324 | 0.0023813 | 0.0000887 | 0.0000009 | ENSG00000064490 | RFXANK | protein_coding | -1.6020062 |
| DEXSeq | ENST00000366285 | 0.0239893 | 0.0025614 | 0.0000509 | ENSG00000171792 | RHNO1 | protein_coding | 0.9507221 |
| DEXSeq | ENST00000591292 | 0.0154944 | 0.0018851 | 0.0000187 | ENSG00000067836 | ROGDI | retained_intron | 1.0774540 |
| DEXSeq | ENST00000520237 | 0.0060789 | 0.0003924 | 0.0000039 | ENSG00000174093 | RP11-1407O15.2 | protein_coding | 0.9274266 |
| DEXSeq | ENST00000529127 | 0.0323076 | 0.0048136 | 0.0000957 | ENSG00000254746 | RP11-958J22.1 | retained_intron | 0.6497546 |
| DEXSeq | ENST00000401447 | 0.0044390 | 0.0003802 | 0.0000025 | ENSG00000106399 | RPA3 | protein_coding | 2.2442945 |
| DEXSeq | ENST00000506581 | 0.0000000 | 0.0000000 | 0.0000000 | ENSG00000163682 | RPL9 | protein_coding | -2.7999395 |
| DEXSeq | ENST00000295955 | 0.0000000 | 0.0000000 | 0.0000000 | ENSG00000163682 | RPL9 | protein_coding | 2.7997195 |
| DEXSeq | ENST00000300738 | 0.0295711 | 0.0117854 | 0.0000781 | ENSG00000167325 | RRM1 | protein_coding | -1.1121224 |
| DEXSeq | ENST00000454950 | 0.0028913 | 0.0001938 | 0.0000013 | ENSG00000204130 | RUFY2 | protein_coding | -0.7371014 |
| DEXSeq | ENST00000515816 | 0.0151888 | 0.0018857 | 0.0000187 | ENSG00000167100 | SAMD14 | retained_intron | 1.8680468 |
| DEXSeq | ENST00000285206 | 0.0151888 | 0.0079494 | 0.0000790 | ENSG00000167100 | SAMD14 | protein_coding | -1.0811342 |
| DEXSeq | ENST00000460767 | 0.0168103 | 0.0035687 | 0.0000236 | ENSG00000227500 | SCAMP4 | processed_transcript | 0.9720335 |
| DEXSeq | ENST00000397174 | 0.0420357 | 0.0179557 | 0.0001785 | ENSG00000010803 | SCMH1 | protein_coding | 3.1137296 |
| DEXSeq | ENST00000400358 | 0.0494487 | 0.0154758 | 0.0003076 | ENSG00000167037 | SGSM1 | protein_coding | -0.9642964 |
| DEXSeq | ENST00000470591 | 0.0494487 | 0.0281381 | 0.0005594 | ENSG00000167037 | SGSM1 | processed_transcript | 0.9012776 |
| DEXSeq | ENST00000558583 | 0.0278738 | 0.0000000 | 0.0000688 | ENSG00000237515 | SHISA9 | protein_coding | -0.7594214 |
| DEXSeq | ENST00000423335 | 0.0278738 | 0.0000000 | 0.0001307 | ENSG00000237515 | SHISA9 | protein_coding | 0.7580920 |
| DEXSeq | ENST00000378536 | 0.0123341 | 0.0004747 | 0.0000094 | ENSG00000157933 | SKI | protein_coding | -0.9396948 |
| DEXSeq | ENST00000508416 | 0.0123341 | 0.0220655 | 0.0004386 | ENSG00000157933 | SKI | processed_transcript | 0.9253961 |
| DEXSeq | ENST00000483348 | 0.0404366 | 0.0085358 | 0.0001697 | ENSG00000163950 | SLBP | protein_coding | -1.4227994 |
| DEXSeq | ENST00000535347 | 0.0429193 | 0.0189730 | 0.0001886 | ENSG00000111181 | SLC6A12 | protein_coding | -1.5441100 |
| DEXSeq | ENST00000280612 | 0.0228782 | 0.0000000 | 0.0000457 | ENSG00000151012 | SLC7A11 | protein_coding | -1.6838039 |
| DEXSeq | ENST00000509248 | 0.0228782 | 0.0000000 | 0.0000621 | ENSG00000151012 | SLC7A11 | nonsense_mediated_decay | 1.6834652 |
| DEXSeq | ENST00000555678 | 0.0000037 | 0.0000000 | 0.0000000 | ENSG00000155465 | SLC7A7 | retained_intron | 2.3905072 |
| DEXSeq | ENST00000506626 | 0.0011370 | 0.0000367 | 0.0000004 | ENSG00000170365 | SMAD1 | processed_transcript | 1.7191008 |
| DEXSeq | ENST00000221448 | 0.0035053 | 0.0003655 | 0.0000018 | ENSG00000104852 | SNRNP70 | protein_coding | -0.6158515 |
| DEXSeq | ENST00000308527 | 0.0335654 | 0.0000000 | 0.0001094 | ENSG00000173548 | SNX33 | protein_coding | 2.0169757 |
| DEXSeq | ENST00000569152 | 0.0335654 | 0.0000000 | 0.0002290 | ENSG00000173548 | SNX33 | protein_coding | -2.0347800 |
| DEXSeq | ENST00000585725 | 0.0488837 | 0.0440747 | 0.0002921 | ENSG00000005206 | SPPL2B | processed_transcript | 0.5945806 |
| DEXSeq | ENST00000581656 | 0.0030594 | 0.0001443 | 0.0000014 | ENSG00000017373 | SRCIN1 | processed_transcript | 1.0084271 |
| DEXSeq | ENST00000264659 | 0.0030594 | 0.0001804 | 0.0000018 | ENSG00000017373 | SRCIN1 | protein_coding | -0.8672747 |
| DEXSeq | ENST00000579954 | 0.0200768 | 0.0053839 | 0.0000357 | ENSG00000141298 | SSH2 | protein_coding | 0.8244015 |
| DEXSeq | ENST00000361392 | 0.0486388 | 0.0000000 | 0.0002894 | ENSG00000126091 | ST3GAL3 | protein_coding | -2.3079525 |
| DEXSeq | ENST00000361400 | 0.0486388 | 0.0000000 | 0.0003570 | ENSG00000126091 | ST3GAL3 | protein_coding | 2.3104406 |
| DEXSeq | ENST00000528605 | 0.0460386 | 0.0130927 | 0.0002603 | ENSG00000110080 | ST3GAL4 | retained_intron | 1.2554520 |
| DEXSeq | ENST00000461054 | 0.0323084 | 0.0102693 | 0.0001021 | ENSG00000143093 | STRIP1 | processed_transcript | 0.9756518 |
| DEXSeq | ENST00000369902 | 0.0492358 | 0.0152256 | 0.0003027 | ENSG00000107882 | SUFU | protein_coding | -0.8908526 |
| DEXSeq | ENST00000471000 | 0.0492358 | 0.0203802 | 0.0004051 | ENSG00000107882 | SUFU | processed_transcript | 1.0738196 |
| DEXSeq | ENST00000547586 | 0.0352934 | 0.0268192 | 0.0001333 | ENSG00000139531 | SUOX | protein_coding | 4.9233435 |
| DEXSeq | ENST00000532433 | 0.0452667 | 0.0344020 | 0.0002280 | ENSG00000203705 | TATDN3 | retained_intron | 1.0016411 |
| DEXSeq | ENST00000476978 | 0.0250586 | 0.0028622 | 0.0000569 | ENSG00000204219 | TCEA3 | protein_coding | 1.1565087 |
| DEXSeq | ENST00000491186 | 0.0458096 | 0.0249170 | 0.0002477 | ENSG00000213123 | TCTEX1D2 | processed_transcript | 1.0182622 |
| DEXSeq | ENST00000552403 | 0.0334403 | 0.0117918 | 0.0001172 | ENSG00000111077 | TENC1 | retained_intron | 0.7131749 |
| DEXSeq | ENST00000314250 | 0.0334403 | 0.0238267 | 0.0002368 | ENSG00000111077 | TENC1 | protein_coding | -0.7314882 |
| DEXSeq | ENST00000527851 | 0.0199044 | 0.0077100 | 0.0000383 | ENSG00000149809 | TM7SF2 | retained_intron | 1.3804889 |
| DEXSeq | ENST00000503148 | 0.0448667 | 0.0217288 | 0.0002160 | ENSG00000198498 | TMA16 | retained_intron | 1.3047104 |
| DEXSeq | ENST00000437139 | 0.0339230 | 0.0054755 | 0.0001088 | ENSG00000179029 | TMEM107 | protein_coding | -1.0936620 |
| DEXSeq | ENST00000480360 | 0.0452149 | 0.0216728 | 0.0002154 | ENSG00000168936 | TMEM129 | nonsense_mediated_decay | 1.0847372 |
| DEXSeq | ENST00000597370 | 0.0198987 | 0.0076090 | 0.0000378 | ENSG00000161558 | TMEM143 | nonsense_mediated_decay | 3.0577247 |
| DEXSeq | ENST00000565468 | 0.0459439 | 0.0000000 | 0.0002518 | ENSG00000261115 | TMEM178B | protein_coding | -0.9755069 |
| DEXSeq | ENST00000563442 | 0.0459439 | 0.0000000 | 0.0002819 | ENSG00000261115 | TMEM178B | retained_intron | 0.9756545 |
| DEXSeq | ENST00000361906 | 0.0338015 | 0.0109958 | 0.0001093 | ENSG00000198792 | TMEM184B | protein_coding | -1.3119099 |
| DEXSeq | ENST00000361684 | 0.0338015 | 0.0118871 | 0.0001182 | ENSG00000198792 | TMEM184B | protein_coding | 1.0682281 |
| DEXSeq | ENST00000598660 | 0.0394813 | 0.0165702 | 0.0001647 | ENSG00000105696 | TMEM59L | retained_intron | 0.8458150 |
| DEXSeq | ENST00000321196 | 0.0492546 | 0.0464287 | 0.0003077 | ENSG00000179104 | TMTC2 | protein_coding | -0.8001813 |
| DEXSeq | ENST00000375887 | 0.0281199 | 0.0071222 | 0.0000708 | ENSG00000102524 | TNFSF13B | protein_coding | -0.9180277 |
| DEXSeq | ENST00000441818 | 0.0362586 | 0.0146770 | 0.0001459 | ENSG00000100416 | TRMU | nonsense_mediated_decay | -0.8367554 |
| DEXSeq | ENST00000463646 | 0.0131232 | 0.0005376 | 0.0000107 | ENSG00000165125 | TRPV6 | retained_intron | -1.2879529 |
| DEXSeq | ENST00000485138 | 0.0131232 | 0.0012983 | 0.0000258 | ENSG00000165125 | TRPV6 | retained_intron | 1.7171188 |
| DEXSeq | ENST00000463601 | 0.0201771 | 0.0017785 | 0.0000354 | ENSG00000103197 | TSC2 | retained_intron | 1.1114886 |
| DEXSeq | ENST00000498097 | 0.0322999 | 0.0095446 | 0.0000949 | ENSG00000135951 | TSGA10 | processed_transcript | 0.7930141 |
| DEXSeq | ENST00000373290 | 0.0161307 | 0.0000000 | 0.0000175 | ENSG00000099282 | TSPAN15 | protein_coding | -2.6575264 |
| DEXSeq | ENST00000475069 | 0.0161307 | 0.0000000 | 0.0000272 | ENSG00000099282 | TSPAN15 | retained_intron | 2.6601275 |
| DEXSeq | ENST00000258796 | 0.0160997 | 0.0008994 | 0.0000179 | ENSG00000136295 | TTYH3 | protein_coding | -1.1483685 |
| DEXSeq | ENST00000400376 | 0.0160997 | 0.0022908 | 0.0000455 | ENSG00000136295 | TTYH3 | protein_coding | 1.0650193 |
| DEXSeq | ENST00000503506 | 0.0137322 | 0.0013298 | 0.0000132 | ENSG00000198431 | TXNRD1 | protein_coding | -1.6591122 |
| DEXSeq | ENST00000354940 | 0.0137322 | 0.0163981 | 0.0001630 | ENSG00000198431 | TXNRD1 | protein_coding | 1.0612903 |
| DEXSeq | ENST00000460562 | 0.0046301 | 0.0002759 | 0.0000027 | ENSG00000134882 | UBAC2 | processed_transcript | 1.0422158 |
| DEXSeq | ENST00000494576 | 0.0046301 | 0.0258230 | 0.0002567 | ENSG00000134882 | UBAC2 | processed_transcript | -1.5950497 |
| DEXSeq | ENST00000345496 | 0.0491443 | 0.0301504 | 0.0002997 | ENSG00000184787 | UBE2G2 | protein_coding | -0.7539220 |
| DEXSeq | ENST00000397514 | 0.0355049 | 0.0000000 | 0.0001367 | ENSG00000103275 | UBE2I | protein_coding | -0.5250603 |
| DEXSeq | ENST00000406620 | 0.0355049 | 0.0000000 | 0.0002082 | ENSG00000103275 | UBE2I | protein_coding | 0.5253241 |
| DEXSeq | ENST00000488418 | 0.0089759 | 0.0009026 | 0.0000060 | ENSG00000160087 | UBE2J2 | protein_coding | 1.3163608 |
| DEXSeq | ENST00000369908 | 0.0441286 | 0.0310703 | 0.0002059 | ENSG00000198276 | UCKL1 | protein_coding | 0.8754907 |
| DEXSeq | ENST00000279907 | 0.0450306 | 0.0119109 | 0.0002368 | ENSG00000111647 | UHRF1BP1L | protein_coding | -0.5430137 |
| DEXSeq | ENST00000484980 | 0.0318335 | 0.0147031 | 0.0000974 | ENSG00000109103 | UNC119 | protein_coding | 0.8847405 |
| DEXSeq | ENST00000283713 | 0.0452593 | 0.0354084 | 0.0002346 | ENSG00000136059 | VILL | protein_coding | 2.1991012 |
| DEXSeq | ENST00000573314 | 0.0249875 | 0.0083762 | 0.0000555 | ENSG00000138614 | VWA9 | nonsense_mediated_decay | -1.8103804 |
| DEXSeq | ENST00000375128 | 0.0215763 | 0.0042860 | 0.0000426 | ENSG00000136936 | XPA | protein_coding | -1.1807830 |
| DEXSeq | ENST00000223273 | 0.0012262 | 0.0000183 | 0.0000004 | ENSG00000241127 | YAE1D1 | protein_coding | -1.1181848 |
| DEXSeq | ENST00000469737 | 0.0012262 | 0.0117934 | 0.0002344 | ENSG00000241127 | YAE1D1 | processed_transcript | 0.9670990 |
| DEXSeq | ENST00000474392 | 0.0012262 | 0.0240464 | 0.0004780 | ENSG00000241127 | YAE1D1 | retained_intron | 0.9716046 |
| DEXSeq | ENST00000335953 | 0.0181612 | 0.0000000 | 0.0000273 | ENSG00000109906 | ZBTB16 | protein_coding | -0.8864832 |
| DEXSeq | ENST00000545851 | 0.0181612 | 0.0000000 | 0.0000342 | ENSG00000109906 | ZBTB16 | processed_transcript | 0.8865920 |
| DEXSeq | ENST00000370854 | 0.0337987 | 0.0176255 | 0.0001168 | ENSG00000171307 | ZDHHC16 | protein_coding | -2.3737700 |
| DEXSeq | ENST00000533216 | 0.0163053 | 0.0011336 | 0.0000225 | ENSG00000162300 | ZFPL1 | retained_intron | 1.3161995 |
| DEXSeq | ENST00000357182 | 0.0456652 | 0.0125326 | 0.0002491 | ENSG00000163867 | ZMYM6 | protein_coding | -1.0265644 |
| DEXSeq | ENST00000259395 | 0.0199776 | 0.0018850 | 0.0000375 | ENSG00000136870 | ZNF189 | protein_coding | 0.7442631 |
| DEXSeq | ENST00000594012 | 0.0013311 | 0.0000182 | 0.0000004 | ENSG00000198521 | ZNF43 | protein_coding | -0.8022288 |
| DEXSeq | ENST00000598288 | 0.0013311 | 0.0003298 | 0.0000066 | ENSG00000198521 | ZNF43 | protein_coding | 0.6428067 |
| DEXSeq | ENST00000361807 | 0.0309112 | 0.0000000 | 0.0000885 | ENSG00000198298 | ZNF485 | protein_coding | -4.1677474 |
| DEXSeq | ENST00000374435 | 0.0309112 | 0.0000000 | 0.0002572 | ENSG00000198298 | ZNF485 | protein_coding | 4.1527983 |
| DEXSeq | ENST00000458270 | 0.0430037 | 0.0093983 | 0.0001868 | ENSG00000183309 | ZNF623 | protein_coding | 1.1258107 |
| DEXSeq | ENST00000601935 | 0.0454195 | 0.0471526 | 0.0002343 | ENSG00000197372 | ZNF675 | protein_coding | 0.5916161 |
| DEXSeq | ENST00000566625 | 0.0098260 | 0.0007075 | 0.0000070 | ENSG00000179965 | ZNF771 | protein_coding | 1.3342531 |
| DEXSeq | ENST00000563508 | 0.0352521 | 0.0065219 | 0.0001297 | ENSG00000140265 | ZSCAN29 | processed_transcript | -0.7129352 |
| DEXSeq | ENST00000561661 | 0.0352521 | 0.0381311 | 0.0007580 | ENSG00000140265 | ZSCAN29 | protein_coding | 0.4546207 |